- A - Variable in class etomica.conjugategradient.ConjugateGradients
-
- A - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- A - Variable in class etomica.conjugategradient.SteepestDescent
-
- a - Variable in class etomica.dimer.P1LepsHarmonic
-
- a - Variable in class etomica.math.numerical.PadeApproximation
-
- a - Variable in class etomica.meam.P2EAM
-
- A - Variable in class etomica.meam.ParameterSetMEAM
-
- a - Variable in class etomica.meam.ParameterSetMEAM
-
- A - Variable in class etomica.meam.PotentialCuLREP
-
- a - Variable in class etomica.meam.PotentialEAM
-
- a - Variable in class etomica.meam.PotentialEAM_LS
-
- A - Variable in class etomica.meam.PotentialEFS
-
- A - Variable in class etomica.models.co2.P2CO2Hellmann
-
- a - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- a - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- a - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- a - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- a - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- a - Variable in class etomica.models.water.P2Water4PSoft
-
- A - Variable in class etomica.models.water.PNWaterGCPM
-
- A(double) - Method in class etomica.modules.adsorption.EOSSWPatel
-
- a - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- a - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- A - Variable in class etomica.potential.P2HePCKLJS
-
- a - Static variable in class etomica.potential.P2HePCKLJS
-
- a - Variable in class etomica.potential.P2HSDipole
-
- a - Variable in class etomica.potential.P2LJDipole
-
- A - Variable in class etomica.potential.P2NitrogenHellmann
-
- a - Variable in class etomica.potential.P2ReactionFieldDipole
-
- A - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- A - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- A - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- A - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- A - Variable in class etomica.potential.P3HydrogenManzhos
-
- a - Variable in class etomica.potential.PotentialCalculationPhiSum
-
- a - Static variable in class etomica.statmech.HardSphereFluid
-
- a - Static variable in class etomica.veos.bigdecimal.Euler
-
- a - Static variable in class etomica.veos.bigdecimal.PartitionsP
-
The list of all partitions as a vector.
- a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
-
- a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
-
- a - Variable in class etomica.virial.MCMoveClusterAtomHSTree
-
- a - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
-
- a0 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- a0 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- a0 - Variable in class etomica.meam.PotentialEAM_LS
-
- a0 - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- a0 - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- A0 - Variable in class etomica.potential.P2HeSimplified
-
- a0 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- a0 - Variable in class etomica.potential.P4BondTorsion
-
- a0 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- a0 - Variable in class etomica.potential.Potential2SoftSphericalLS
-
- A0 - Static variable in class etomica.statmech.HardSphereSolid
-
- A1 - Variable in class etomica.dimer.P1LepsHarmonic
-
- A1 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- A1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- A1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- A1(double) - Method in class etomica.modules.adsorption.EOSSWPatel
-
- A1 - Variable in class etomica.potential.P2HeSimplified
-
- a1 - Variable in class etomica.potential.P2QChemInterpolated
-
- a1 - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
-
- a1 - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
-
- a1 - Variable in class etomica.potential.P3QChem.DampingParams
-
- a1 - Variable in class etomica.potential.P4BondTorsion
-
- a1 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- a1 - Variable in class etomica.virial.B3ForSphericallySymmetricU.DampingParams
-
- A2 - Variable in class etomica.dimer.P1LepsHarmonic
-
- a2 - Variable in class etomica.meam.P2EAM
-
- A2 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- A2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- A2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- A2 - Variable in class etomica.potential.P2HeSimplified
-
- a2 - Variable in class etomica.potential.P2QChemInterpolated
-
- a2 - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
-
- a2 - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
-
- a2 - Variable in class etomica.potential.P3QChem.DampingParams
-
- a2 - Variable in class etomica.potential.P4BondTorsion
-
- a2 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- a2 - Variable in class etomica.virial.B3ForSphericallySymmetricU.DampingParams
-
- A3 - Variable in class etomica.potential.P2HeSimplified
-
- a3 - Variable in class etomica.potential.P4BondTorsion
-
- a3 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- AA - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- AA - Static variable in class etomica.potential.P2NitrogenHellmann
-
- AAbonded - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- AAlphaFunction(int, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
-
- aam - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- aamOriented - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- AandPAlpha(double, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
-
- AandPBeta(double, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
-
- ab - Variable in class etomica.lattice.crystal.PrimitiveHexagonal
-
- ab - Variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- AB - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- AB - Static variable in class etomica.potential.P2NitrogenHellmann
-
- ABbonded - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- ABbonded - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- ABetaFunction(int, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
-
- abicipeso4(double, double, double, double) - Static method in class etomica.potential.P2O2Bartolomei
-
- AbnormalCompletionException - Exception in etomica.exception
-
Exception that indicates a method is defined for a class (perhaps to adhere
to an interface), but its implementation is not yet completed.
- AbnormalCompletionException() - Constructor for exception etomica.exception.AbnormalCompletionException
-
Constructor for AbnormalCompletionException
- AbnormalCompletionException(String) - Constructor for exception etomica.exception.AbnormalCompletionException
-
Constructor for MethodNotImplementedException.
- aBonds - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- AboutBoxWindow - Class in etomica.graphics
-
- AboutBoxWindow(Component, String) - Constructor for class etomica.graphics.AboutBoxWindow
-
- AboutBoxWindow(Component) - Constructor for class etomica.graphics.AboutBoxWindow
-
- AboutBoxWindow(Component, String, String[], String[]) - Constructor for class etomica.graphics.AboutBoxWindow
-
- abParams - Variable in class etomica.graph.operations.MaxIsomorphWertheim.MaxIsomorphWertheimParameters
-
- Abs() - Constructor for class etomica.math.function.Function.Abs
-
- abs() - Method in class etomica.veos.bigdecimal.BigSurd
-
Absolute value.
- abs() - Method in class etomica.veos.bigdecimal.Rational
-
Absolute value.
- AbstractBitmap - Class in etomica.graph.model.impl
-
- AbstractBitmap() - Constructor for class etomica.graph.model.impl.AbstractBitmap
-
- AbstractLattice - Interface in etomica.lattice
-
Interface for a generic lattice, which is a collection of sites that can be
accessed individually via specification of a set of integers.
- AbstractOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.AbstractOptionHandler
-
- AbstractSearchState - Class in etomica.graph.isomorphism
-
- AbstractSearchState() - Constructor for class etomica.graph.isomorphism.AbstractSearchState
-
- AbstractSearchState(Graph, Graph) - Constructor for class etomica.graph.isomorphism.AbstractSearchState
-
- AbstractTraversal - Class in etomica.graph.traversal
-
- AbstractTraversal() - Constructor for class etomica.graph.traversal.AbstractTraversal
-
- ac - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
-
- ac - Variable in class etomica.modules.multiharmonic.DataProcessorVar
-
- acc - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- acc - Variable in class etomica.modules.statistics.DataAccDiffCorrectedPusher
-
- acc - Variable in class etomica.modules.statistics.DataAccDifficultyPusher
-
- acc - Variable in class etomica.modules.statistics.DataAccSamplesPusher
-
- acc - Variable in class etomica.overlap.DataOverlap.DataSourceOverlapAvgSimple
-
- accept(Graph) - Method in class etomica.graph.iterators.filters.FieldNodeCount
-
- accept(Graph, Set<Graph>) - Method in class etomica.graph.iterators.filters.GlobalFilter
-
- accept(Graph, Set<Graph>) - Method in class etomica.graph.iterators.filters.IdenticalGraphFilter
-
- accept(Graph, Set<Graph>) - Method in class etomica.graph.iterators.filters.IsomorphismFilter
-
- accept(Graph) - Method in class etomica.graph.iterators.filters.LocalFilter
-
- accept(Graph) - Method in class etomica.graph.iterators.filters.PropertyFilter
-
- accept(File) - Method in class etomica.graph.view.rasterizer.SVGConverter.SVGFileFilter
-
- accept(IAtomList) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
-
- accept(IAtomList) - Method in class etomica.modules.pistoncylinder.ApiFilteredCylinder.AtomFilterInCylinder
-
- accept(IAtomList) - Method in class etomica.modules.render.RenderMD.CriterionCar
-
- accept(IAtomList) - Method in class etomica.modules.sam.CriterionTether3
-
- accept(IAtomList) - Method in class etomica.nbr.CriterionAdapter
-
Implementation of this method should introduce new criterion and return
true if pair meets this criterion and that of the wrapped
NeighborCriterion.
- accept(IAtomList) - Method in class etomica.nbr.CriterionAll
-
Always returns true, indicating that all atoms pairs are neighbors.
- accept(IAtomList) - Method in class etomica.nbr.CriterionBondedSimple
-
- accept(IAtomList) - Method in class etomica.nbr.CriterionInterMolecular
-
- accept(IAtomList) - Method in class etomica.nbr.CriterionMolecular
-
Returns false if pair is/isn't in same molecule (depending on setting
of intraMolecular); if matches this criterion, return value will be
that given by any subCriterion.
- accept(IAtomList) - Method in class etomica.nbr.CriterionMolecularNonAdjacent
-
- accept(IAtomList) - Method in class etomica.nbr.CriterionNone
-
Always returns false, indicating that no atoms pairs are neighbors.
- accept(IAtomList) - Method in class etomica.nbr.CriterionPositionWall
-
- accept(IAtomList) - Method in class etomica.nbr.CriterionSimple
-
- accept(IAtomList) - Method in class etomica.nbr.CriterionType
-
Returns true if the AtomType of the atom matches the AtomType given at
construction and if the wrapped criterion accept also returns true.
- accept(IAtomList) - Method in class etomica.nbr.CriterionTypePair
-
Returns true if the AtomTypes for the pair of atoms match the AtomTypes
given at construction (without regard to the order of the pair), and if
the wrapped criterion also accepts the pair.
- accept(IAtomList) - Method in class etomica.nbr.CriterionTypesCombination
-
Returns true if the AtomTypes for the pair of atoms match the AtomTypes
given at construction (without regard to the order of the AtomSet), and
if the wrapped criterion also accepts the AtomSet.
- accept(IAtomList) - Method in class etomica.nbr.CriterionTypesMulti
-
Returns true if the AtomTypes for the pair of atoms match the AtomTypes
given at construction (without regard to the order of the AtomSet), and
if the wrapped criterion also accepts the AtomSet.
- accept(IMoleculeList) - Method in class etomica.nbr.molecule.CriterionAdapterMolecular
-
Implementation of this method should introduce new criterion and return
true if pair meets this criterion and that of the wrapped
NeighborCriterion.
- accept(IMoleculeList) - Method in class etomica.nbr.molecule.CriterionAllMolecular
-
Always returns true, indicating that all atoms pairs are neighbors.
- accept(IMoleculeList) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- accept(IMoleculeList) - Method in class etomica.nbr.molecule.CriterionSpecies
-
Returns true if the species of the molecule matches the Species given at
construction and if the wrapped criterion accept also returns true.
- accept(IMoleculeList) - Method in class etomica.nbr.molecule.CriterionSpeciesPair
-
Returns true if the Species for the pair of molecules match the Species
given at construction (without regard to the order of the pair), and if
the wrapped criterion also accepts the pair.
- accept(IMoleculeList) - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular
-
- accept(IAtomList) - Method in interface etomica.nbr.NeighborCriterion
-
- acceptanceProbability() - Method in class etomica.integrator.mcmove.MCMoveTracker
-
Returns the average probability of accepting the move associated with
this tracker.
- acceptanceRatio() - Method in class etomica.integrator.mcmove.MCMoveTracker
-
Returns the fraction of accepted trials of the move associated with
this tracker.
- acceptanceTarget - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
-
- acceptNotify() - Method in class etomica.association.MCMoveBiasUB
-
- acceptNotify() - Method in class etomica.association.MCMoveBiasUBMolecule
-
- acceptNotify() - Method in class etomica.association.MCMoveDimer
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.association.MCMoveDimerRotate
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.association.MCMoveSmer
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.association.MCMoveSmerRotate
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.association.MCMoveVolumeAssociated
-
- acceptNotify() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- acceptNotify() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMove
-
Method called by IntegratorMC in the event that the most recent trial is
accepted.
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveAtom
-
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
-
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveDimer
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
-
Swaps positions of molecules in two boxes.
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- acceptNotify() - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
-
- acceptNotify() - Method in class etomica.models.hexane.MCMoveCBMC
-
- acceptNotify() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- acceptNotify() - Method in class etomica.models.hexane.MCMoveReptate
-
- acceptNotify() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- acceptNotify() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- acceptNotify() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- acceptNotify() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- acceptNotify() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- acceptNotify() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- acceptNotify() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- acceptNotify() - Method in class etomica.modules.adsorption.MyMCMove
-
- acceptNotify() - Method in class etomica.modules.dcvgcmd.MyMCMove
-
- acceptNotify() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveAtomCoupled
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.normalmode.MCMoveAtomSuperBox
-
Method called by IntegratorMC in the event that the most recent trial is accepted.
- acceptNotify() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveHarmonic
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveHarmonicStep
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
- acceptNotify() - Method in class etomica.normalmode.MCMovePhaseAngle
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveSingleMode
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- acceptNotify() - Method in class etomica.normalmode.MCMoveWV
-
- acceptNotify() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- acceptNotify() - Method in class etomica.spin.MCMoveSpinFlip
-
- acceptNotify() - Method in class etomica.virial.BoxCluster
-
Informs the box that the trial was accepted so it will keep the new
coordinate pairs.
- acceptNotify() - Method in class etomica.virial.MCMoveChangeBondLength
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterAngleBend
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterAtom
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomHSChain
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomHSTree
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomMulti
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomQ
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterDiagram
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterMolecule
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterMoleculeMulti
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraChain
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraTree
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterRingRegrow
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterRingScale
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterRotateCH3
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- acceptNotify() - Method in class etomica.virial.MCMoveClusterWiggleMulti
-
- acceptNotify() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
-
Swaps positions of molecules in two boxes.
- accRefUa2 - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
-
- accTargetUa2 - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
-
- accumulator - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- accumulator - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- accumulator - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- accumulator - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- accumulator - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- accumulator - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- accumulator - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- accumulator - Variable in class etomica.virial.simulations.SimulationVirial
-
- accumulator1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- accumulator2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- accumulatorAction - Variable in class etomica.action.SimulationRestart
-
- AccumulatorAverage - Class in etomica.data
-
Accumulator that keeps statistics for averaging and error analysis.
- AccumulatorAverage() - Constructor for class etomica.data.AccumulatorAverage
-
Default constructor sets block size to 1000 and sets the
interval for pushing the output data (pushInterval) to 100.
- AccumulatorAverage(long) - Constructor for class etomica.data.AccumulatorAverage
-
Constructs with interval for pushing the output data set to 100.
- accumulatorAverage - Variable in class etomica.graphics.DisplayTextBoxesCAE
-
- AccumulatorAverage.StatType - Class in etomica.data
-
Enumerated type that can be used to indicate the statistic to be taken
from the accumulator (e.g., average, error, current value, etc.).
- AccumulatorAverageBlockless - Class in etomica.data
-
AccumulatorAverage that does not use blocks (best used when each sample
is independent).
- AccumulatorAverageBlockless() - Constructor for class etomica.data.AccumulatorAverageBlockless
-
Default constructor sets block size to Default value, and sets the
interval for pushing the output data (pushInterval) to 100.
- AccumulatorAverageBlockless.AllData - Class in etomica.data
-
- AccumulatorAverageBlockless.StatType - Class in etomica.data
-
Enumerated type that can be used to indicated the statistic to be taken
from the accumulator (e.g., average, error, current value, etc.).
- AccumulatorAverageBlocklessSlim - Class in etomica.data
-
AccumulatorAverage that does not use blocks (best used when each sample
is independent).
- AccumulatorAverageBlocklessSlim() - Constructor for class etomica.data.AccumulatorAverageBlocklessSlim
-
- AccumulatorAverageBlocklessSlim.StatType - Class in etomica.data
-
Enumerated type that can be used to indicated the statistic to be taken
from the accumulator (e.g., average, error, current value, etc.).
- AccumulatorAverageBootstrap - Class in etomica.data
-
AccumulatorAverage that keeps track of block averages and standard
deviations corresponding to all block sizes from 1 to the n where n is the
largest power of 2 less than the current number of samples.
- AccumulatorAverageBootstrap() - Constructor for class etomica.data.AccumulatorAverageBootstrap
-
- AccumulatorAverageBootstrap(int) - Constructor for class etomica.data.AccumulatorAverageBootstrap
-
With this constructor, the accumulator will use an internal RNG with a
set seed such that each resampling of the data will be identical (the
same set of samples will go into the averages and the standard
deviations, etc).
- AccumulatorAverageBootstrap(IRandom) - Constructor for class etomica.data.AccumulatorAverageBootstrap
-
- AccumulatorAverageBootstrap(IRandom, int) - Constructor for class etomica.data.AccumulatorAverageBootstrap
-
- AccumulatorAverageBootstrap.HistogramFactory - Interface in etomica.data
-
- AccumulatorAverageCollapsing - Class in etomica.data
-
AccumulatorAverage that adjusts the block size during the simulation.
- AccumulatorAverageCollapsing() - Constructor for class etomica.data.AccumulatorAverageCollapsing
-
Default constructor sets the maximum number of blocks (maxBlocks) to a default value of 20,
the initial block size (blockSize) to 1 and the interval for pushing the output data (pushInterval)
to 100.
- AccumulatorAverageCollapsing(int) - Constructor for class etomica.data.AccumulatorAverageCollapsing
-
Constructor with default pushInterval of 100 and initial blockSize of 1.
- AccumulatorAverageCollapsing(int, int) - Constructor for class etomica.data.AccumulatorAverageCollapsing
-
Constructor with default pushInterval of 100.
- AccumulatorAverageCollapsingLog - Class in etomica.data
-
AccumulatorAverage that keeps track of block averages and standard
deviations corresponding to all block sizes from 1 to the n where n is the
largest power of 2 less than the current number of samples.
- AccumulatorAverageCollapsingLog() - Constructor for class etomica.data.AccumulatorAverageCollapsingLog
-
- AccumulatorAverageCollapsingLog(int) - Constructor for class etomica.data.AccumulatorAverageCollapsingLog
-
With this constructor, the accumulator will use an internal RNG with a
set seed such that each resampling of the data will be identical (the
same set of samples will go into the averages and the standard
deviations, etc).
- AccumulatorAverageCollapsingLog(IRandom) - Constructor for class etomica.data.AccumulatorAverageCollapsingLog
-
- AccumulatorAverageCollapsingLog(IRandom, int) - Constructor for class etomica.data.AccumulatorAverageCollapsingLog
-
- AccumulatorAverageCollapsingLogAB - Class in etomica.data
-
- AccumulatorAverageCollapsingLogAB() - Constructor for class etomica.data.AccumulatorAverageCollapsingLogAB
-
- AccumulatorAverageCollapsingLogAB(IRandom) - Constructor for class etomica.data.AccumulatorAverageCollapsingLogAB
-
- AccumulatorAverageCovariance - Class in etomica.data
-
Class that does the work of AccumulatorAverageFixed and also calculates the
covariance of the incoming data values (the covariance of each value with
each other value, as well as itself (which is actually its standard
deviation)) as well as the covariance of the block averages of the different
data quantities.
- AccumulatorAverageCovariance() - Constructor for class etomica.data.AccumulatorAverageCovariance
-
- AccumulatorAverageCovariance(boolean) - Constructor for class etomica.data.AccumulatorAverageCovariance
-
- AccumulatorAverageCovariance(long) - Constructor for class etomica.data.AccumulatorAverageCovariance
-
- AccumulatorAverageCovariance(long, boolean) - Constructor for class etomica.data.AccumulatorAverageCovariance
-
- AccumulatorAverageFixed - Class in etomica.data
-
AccumulatorAverage that maintains a fixed block size.
- AccumulatorAverageFixed() - Constructor for class etomica.data.AccumulatorAverageFixed
-
Default constructor sets block size to 1000 and sets the
interval for pushing the output data (pushInterval) to 100.
- AccumulatorAverageFixed(long) - Constructor for class etomica.data.AccumulatorAverageFixed
-
Constructs with interval for pushing the output data set to 100.
- AccumulatorAverageFixedOutputFile - Class in etomica.data
-
AccumulatorAverage that maintains a fixed block size.
- AccumulatorAverageFixedOutputFile() - Constructor for class etomica.data.AccumulatorAverageFixedOutputFile
-
Default constructor sets block size to Default value, and sets the
interval for pushing the output data (pushInterval) to 100.
- AccumulatorAverageFixedOutputFile(int) - Constructor for class etomica.data.AccumulatorAverageFixedOutputFile
-
- AccumulatorCounter - Class in etomica.data
-
Data processor that simply counts the number of times its
addData method is invoked.
- AccumulatorCounter() - Constructor for class etomica.data.AccumulatorCounter
-
- AccumulatorFactory - Interface in etomica.modules.statistics
-
- AccumulatorHistogram - Class in etomica.data
-
Accumulator that keeps histogram of data.
- AccumulatorHistogram() - Constructor for class etomica.data.AccumulatorHistogram
-
Creates instance using HistogramSimple factory and specifying histograms
having 100 bins.
- AccumulatorHistogram(Histogram) - Constructor for class etomica.data.AccumulatorHistogram
-
Creates instance using given histogram factory with default nBins of 100.
- AccumulatorHistogram(Histogram, int) - Constructor for class etomica.data.AccumulatorHistogram
-
Creates instance using the given histogram factory making histograms having
the given number of bins.
- AccumulatorHistory - Class in etomica.data
-
Accumulator that keeps history of data.
- AccumulatorHistory() - Constructor for class etomica.data.AccumulatorHistory
-
Creates instance using HistorySimple factory and specifying historys
having 100 bins.
- AccumulatorHistory(History) - Constructor for class etomica.data.AccumulatorHistory
-
- accumulatorHistory - Variable in class etomica.graphics.ActionHistoryWindow
-
- AccumulatorHistory.DataSourceCount - Class in etomica.data
-
Simple DataSource to use as a default time DataSource.
- AccumulatorMimicMu - Class in etomica.modules.statistics
-
- AccumulatorMimicMu(IntegratorBox) - Constructor for class etomica.modules.statistics.AccumulatorMimicMu
-
- AccumulatorOverlapAverageUa2 - Class in etomica.modules.multiharmonic.overlap
-
Accumulator for taking ratio between two sums (and pretend it's an "average")
Data added to this accumulator must be a 2-element DataDoubleArray
- AccumulatorOverlapAverageUa2(int, boolean) - Constructor for class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- accumulatorPE - Variable in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- accumulatorPump - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- accumulatorPump - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- accumulatorPump - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- accumulatorPump - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- accumulatorPump - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- accumulatorPump - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- accumulatorPump - Variable in class etomica.virial.simulations.SimulationVirial
-
- accumulatorPumps - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- accumulatorPumps - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- accumulatorPumps - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- accumulatorPumps - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- accumulatorPumps - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- accumulatorPumps - Variable in class etomica.normalmode.SimOverlap
-
- accumulatorPumps - Variable in class etomica.normalmode.SimOverlapLJ
-
- accumulatorPumps - Variable in class etomica.normalmode.SimOverlapLJModule
-
- accumulatorPumps - Variable in class etomica.normalmode.SimOverlapModule
-
- accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- accumulatorPumps - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- accumulatorPumps - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- accumulatorPumps - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- accumulatorPumps - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- AccumulatorRatioAverageCovariance - Class in etomica.data
-
Accumulator for calculating ratio between sums.
- AccumulatorRatioAverageCovariance() - Constructor for class etomica.data.AccumulatorRatioAverageCovariance
-
- AccumulatorRatioAverageCovariance(long) - Constructor for class etomica.data.AccumulatorRatioAverageCovariance
-
- AccumulatorRatioAverageCovarianceFull - Class in etomica.data
-
Accumulator for calculating ratio between sums.
- AccumulatorRatioAverageCovarianceFull() - Constructor for class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- AccumulatorRatioAverageCovarianceFull(long) - Constructor for class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- accumulators - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- accumulators - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- accumulators - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- accumulators - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- accumulators - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- accumulators - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- accumulators - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- accumulators - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- accumulators - Variable in class etomica.normalmode.SimOverlap
-
- accumulators - Variable in class etomica.normalmode.SimOverlapLJ
-
- accumulators - Variable in class etomica.normalmode.SimOverlapLJModule
-
- accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- accumulators - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- accumulators - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- accumulators - Variable in class etomica.virial.MeterVirialBDBin
-
- accumulators - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- accumulators - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- accumulators - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- AccumulatorVirialOverlapSingleAverage - Class in etomica.virial.overlap
-
Accumulator for taking ratio between two sums (and pretend it's an "average")
Data added to this accumulator must be a 2-element DataDoubleArray
- AccumulatorVirialOverlapSingleAverage(int, boolean) - Constructor for class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- AccumulatorVirialOverlapSingleAverage(long, int, boolean) - Constructor for class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- AceticAcidMCParam() - Constructor for class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
-
- AceticAcidModPotentialHelper - Class in etomica.models.OPLS
-
PotentialHelper class of acetic acid using improved OPLS (or TraPPE) united atom model
- AceticAcidModPotentialHelper() - Constructor for class etomica.models.OPLS.AceticAcidModPotentialHelper
-
- AceticAcidPotentialHelper - Class in etomica.models.OPLS
-
PotentialHelper class of acetic acid using OPLS united atom model
- AceticAcidPotentialHelper() - Constructor for class etomica.models.OPLS.AceticAcidPotentialHelper
-
- ACollectionBondedPotential - Class in etomica.virial.GUI.components
-
- ACollectionBondedPotential() - Constructor for class etomica.virial.GUI.components.ACollectionBondedPotential
-
- acos(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The inverse trigonometric cosine.
- acosh(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The inverse hyperbolic cosine.
- action - Variable in class etomica.action.activity.ControllerEvent
-
- action - Variable in class etomica.util.Grabber.CornerSetListener
-
- ActionConfigWindow - Class in etomica.graphics
-
Action that opens a new window and dumps the coordinates into the window.
- ActionConfigWindow(Box) - Constructor for class etomica.graphics.ActionConfigWindow
-
- ActionCornerSetter(Grabber, int) - Constructor for class etomica.util.Grabber.ActionCornerSetter
-
- ActionGraphic - Class in etomica.graphics
-
Wrapper of an etomica Action that permits it to be used as a java.awt action listener.
- ActionGraphic(IAction) - Constructor for class etomica.graphics.ActionGraphic
-
- ActionGroup - Interface in etomica.action
-
An action formed from a set of other actions.
- ActionGroupSeries - Class in etomica.action
-
A set of Action instances grouped and performed in series
as if a single action.
- ActionGroupSeries() - Constructor for class etomica.action.ActionGroupSeries
-
Constructs an action group that holds no actions.
- ActionGroupSeries(IAction[]) - Constructor for class etomica.action.ActionGroupSeries
-
Defines group via the given array of actions.
- actionHash - Variable in class etomica.graphics.DeviceSelector
-
- ActionHistoryWindow - Class in etomica.graphics
-
Action that opens a new window and dumps the coordinates into the window.
- ActionHistoryWindow(AccumulatorHistory) - Constructor for class etomica.graphics.ActionHistoryWindow
-
- ActionIntegrate - Class in etomica.action
-
Action that repeatedly invokes an Integrator's doStep method.
- ActionIntegrate(Integrator) - Constructor for class etomica.action.ActionIntegrate
-
Constructs activity to generate configurations with
the given integrator.
- ActionIntegrate(Integrator, boolean) - Constructor for class etomica.action.ActionIntegrate
-
- actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- actionIntegrate - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- actionIntegrator - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- actionIntegrator - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- actionIntegrator - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- actionIntegrator - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- actionIntegrator - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- actionIntegrator - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- ActionMinimizeEnergy - Class in etomica.action
-
- ActionMinimizeEnergy(Space, int, PotentialMaster, Box) - Constructor for class etomica.action.ActionMinimizeEnergy
-
- ActionMinimizeEnergy.MyForceTorque - Class in etomica.action
-
- ActionMoveWall(DeviceSlider, Sam, IAction) - Constructor for class etomica.modules.sam.SamGraphic.ActionMoveWall
-
- actionPerformed() - Method in class etomica.action.ActionGroupSeries
-
Invokes all actions in the group, in the order that they were added at construction and
in previous calls to addAction.
- actionPerformed() - Method in class etomica.action.ActionIntegrate
-
Main loop for conduct of integration.
- actionPerformed() - Method in class etomica.action.ActionMinimizeEnergy
-
- actionPerformed() - Method in class etomica.action.ActionToggle
-
Toggles the state of the target object (true to false, false to true).
- actionPerformed() - Method in class etomica.action.Activity
-
Sets integrator to begin isActive on its own thread.
- actionPerformed(IAtom) - Method in interface etomica.action.AtomAction
-
Performs the defined action on the specified atom
- actionPerformed(IAtom) - Method in class etomica.action.AtomActionRandomizeVelocity
-
Assigns velocity to atom with components selected from a Maxwell-Boltzmann
distribution with temperature most recently set for the action.
- actionPerformed(IAtom) - Method in class etomica.action.AtomActionRotateBy
-
- actionPerformed(IAtom) - Method in class etomica.action.AtomActionTranslateBy
-
- actionPerformed() - Method in class etomica.action.BoxDeleteMolecules
-
Performs the action of deleting test == false molecules, considering
all molecules in the box last given to setBox.
- actionPerformed() - Method in class etomica.action.BoxImposePbc
-
- actionPerformed() - Method in class etomica.action.BoxInflate
-
Performs boundary dimension change
- actionPerformed() - Method in class etomica.action.BoxInflateAnisotropic
-
Performs anisotropic inflation.
- actionPerformed() - Method in class etomica.action.BoxInflateDeformable
-
Performs isotropic inflation.
- actionPerformed() - Method in class etomica.action.BoxQuench
-
- actionPerformed() - Method in class etomica.action.BoxRandomizeMomenta
-
- actionPerformed() - Method in class etomica.action.BoxScaleMomenta
-
- actionPerformed() - Method in class etomica.action.CalcVibrationalModes
-
- actionPerformed() - Method in class etomica.action.ControllerToggle
-
- actionPerformed() - Method in interface etomica.action.IAction
-
Completes the action defined by the class implementing this interface.
- actionPerformed() - Method in class etomica.action.IntegratorReset
-
- actionPerformed(IMolecule) - Method in interface etomica.action.MoleculeAction
-
- actionPerformed(IMolecule) - Method in class etomica.action.MoleculeActionTranslateTo
-
- actionPerformed(IMolecule) - Method in class etomica.action.MoleculeChildAtomAction
-
- actionPerformed() - Method in class etomica.action.PDBWriter
-
- actionPerformed() - Method in class etomica.action.SimulationDataAction
-
- actionPerformed() - Method in class etomica.action.SimulationRestart
-
Resets boxs, integrators, and accumulators.
- actionPerformed() - Method in class etomica.action.WriteConfiguration
-
Writes the leaf Atom coordinates to the file confName.pos_new.
- actionPerformed() - Method in class etomica.action.WriteConfigurationBinary
-
Writes the leaf Atom coordinates to the file confName.pos_new.
- actionPerformed() - Method in class etomica.action.WriteConfigurationDLPOLY
-
Writes the leaf Atom coordinates to the file confName.pos_new.
- actionPerformed() - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
Writes the leaf Atom coordinates to the file CONFIG.
- actionPerformed() - Method in class etomica.action.XYZWriter
-
- actionPerformed(IEvent) - Method in class etomica.association.AssociationManager
-
- actionPerformed(IEvent) - Method in class etomica.association.AssociationManagerMolecule
-
- actionPerformed(IEvent) - Method in class etomica.data.DataLogger
-
Close file when integrator is done.
- actionPerformed() - Method in class etomica.data.DataPump
-
Transmits the data from the source to the sink.
- actionPerformed() - Method in class etomica.data.DataPumpListenerPow
-
- actionPerformed() - Method in class etomica.data.DataPumpListenerSmart
-
- actionPerformed() - Method in class etomica.data.DataStreamAction
-
- actionPerformed(Object) - Method in class etomica.data.DataStreamAction
-
- actionPerformed() - Method in class etomica.data.meter.MeterDihedralAngle
-
Measures the dihedral angle's for the current configuration of the given box.
- actionPerformed() - Method in class etomica.data.meter.MeterRDF
-
Takes the RDF for the current configuration of the given box.
- actionPerformed() - Method in class etomica.data.meter.MeterRDFPC
-
Takes the RDF for the current configuration of the given box.
- actionPerformed() - Method in class etomica.graphics.ActionConfigWindow
-
- actionPerformed(ActionEvent) - Method in class etomica.graphics.ActionGraphic
-
- actionPerformed() - Method in class etomica.graphics.ActionGraphic
-
- actionPerformed() - Method in class etomica.graphics.ActionHistoryWindow
-
- actionPerformed() - Method in class etomica.graphics.ActionVelocityWindow
-
- actionPerformed() - Method in class etomica.graphics.Device.ActionSet
-
- actionPerformed(ActionEvent) - Method in class etomica.graphics.DisplayPlot.DataWriter
-
- actionPerformed(ActionEvent) - Method in class etomica.graphics.DisplayPlot.RawDataWindowOpener
-
- actionPerformed() - Method in class etomica.graphics.DisplayPolytope
-
- actionPerformed(IEvent) - Method in class etomica.integrator.IntegratorPT.BoxTracker
-
Method called when two boxes are successfully exchanged.
- actionPerformed() - Method in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
-
- actionPerformed() - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- actionPerformed(IEvent) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- actionPerformed(IEvent) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- actionPerformed(IEvent) - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- actionPerformed() - Method in class etomica.mappedRdf.MeterMappedRdf
-
Takes the RDF for the current configuration of the given box.
- actionPerformed() - Method in class etomica.mappedvirial.MeterMeanForce
-
- actionPerformed() - Method in class etomica.math.numerical.AkimaSplineSmootherApp.PlotAction
-
- actionPerformed() - Method in class etomica.math.numerical.AkimaSplineSmootherDyApp.PlotAction
-
- actionPerformed() - Method in class etomica.models.hexane.CheckCBMCHexane
-
- actionPerformed() - Method in class etomica.models.hexane.ShowStep
-
- actionPerformed(IAtom) - Method in class etomica.models.nitrogen.AtomActionTransformed
-
- actionPerformed() - Method in class etomica.models.nitrogen.MeterNormalizedCoord
-
Assigning the histogram to data
- actionPerformed() - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta
-
Assigning the histogram to data
- actionPerformed() - Method in class etomica.models.nitrogen.MeterOrientationDistribution
-
Assigning the histogram to data
- actionPerformed() - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup
-
Assigning the histogram to data
- actionPerformed() - Method in class etomica.models.oneDHardRods.WriteHistograms
-
- actionPerformed() - Method in class etomica.modifier.ModifyAction
-
Executes the setValue method of the wrapped modifier, using
the value given in the most recent call to this.setValue.
- actionPerformed() - Method in class etomica.modifier.ModifyBooleanAction
-
- actionPerformed(ActionEvent) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
-
- actionPerformed(ActionEvent) - Method in class etomica.modules.clustergenerator.MyApplet.Stopper
-
- actionPerformed() - Method in class etomica.modules.colloid.ColloidGraphic.GraftAction
-
- actionPerformed() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- actionPerformed() - Method in class etomica.modules.pistoncylinder.ActionPistonUpdate
-
- actionPerformed() - Method in class etomica.modules.sam.SamGraphic.ActionMoveWall
-
- actionPerformed() - Method in class etomica.normalmode.HSNPT.ActionSummer
-
- actionPerformed() - Method in class etomica.normalmode.MeterAtomicDisplacement
-
- actionPerformed() - Method in class etomica.normalmode.MeterNormalMode
-
Calculating things and adds terms to the sums
- actionPerformed() - Method in class etomica.normalmode.MeterTiltHistogram
-
- actionPerformed() - Method in class etomica.normalmode.MeterTiltRotationHistogram
-
- actionPerformed() - Method in class etomica.normalmode.WriteS
-
- actionPerformed(IAtom) - Method in class etomica.paracetamol.AtomActionTransformed
-
- actionPerformed() - Method in class etomica.surfacetension.ActionRecenter
-
- actionPerformed(ActionEvent) - Method in class etomica.util.Grabber.ActionCornerSetter
-
- actionPerformed(E) - Method in interface etomica.util.IListener
-
- actionPerformed(ActionEvent) - Method in class etomica.veos.bigdecimal.Wigner3jGUI
-
Interpreter parser loop.
- actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.controllers.ControllerAlertMsgBox.CloseWindowButtonListener
-
- actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval.NoDoNotRemoveSpeciesButtonListener
-
- actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval.YesRemoveSpeciesButtonListener
-
- actionPerformed(ActionEvent) - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
-
- actionPerformed() - Method in class etomica.virial.MeterVirialBDBin
-
- actionPerformed() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- actionPerformed() - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- actionPerformed() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- actionPerformed(IMolecule) - Method in class etomica.virial.MoleculeActionRelaxWater3P
-
- actionPerformed() - Method in class etomica.zeolite.MSDCoordWriter
-
- actionPerformed(IEvent) - Method in class etomica.zeolite.MSDCoordWriter
-
- actionPerformed() - Method in class etomica.zeolite.ZeoliteSimStart
-
- ActionPistonUpdate - Class in etomica.modules.pistoncylinder
-
Action that informs the integrator that some property of the piston
has changed (pressure, mass, velocity)
- ActionPistonUpdate(IntegratorHardPiston) - Constructor for class etomica.modules.pistoncylinder.ActionPistonUpdate
-
- ActionRecenter - Class in etomica.surfacetension
-
- ActionRecenter(LJMC) - Constructor for class etomica.surfacetension.ActionRecenter
-
- actions - Variable in class etomica.action.activity.ActivityGroupParallel
-
- ActionSet() - Constructor for class etomica.graphics.Device.ActionSet
-
- ActionSummer(Box, Space) - Constructor for class etomica.normalmode.HSNPT.ActionSummer
-
- ActionToggle - Class in etomica.action
-
Action that toggles a boolean value.
- ActionToggle(ModifierBoolean) - Constructor for class etomica.action.ActionToggle
-
- ActionToggle(ModifierBoolean, String, String) - Constructor for class etomica.action.ActionToggle
-
- ActionVelocityWindow - Class in etomica.graphics
-
Action that opens a new window and dumps the velocities into the window.
- ActionVelocityWindow(Box) - Constructor for class etomica.graphics.ActionVelocityWindow
-
- active - Variable in class etomica.data.DataAccumulator
-
Flag specifying whether the manager responds to integrator events
- active - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- active - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- activeCornerSetter - Variable in class etomica.util.Grabber
-
- Activity - Class in etomica.action
-
An Action that supports the capability of pausing/unpausing and terminating
on request.
- Activity() - Constructor for class etomica.action.Activity
-
Create class with a simple default label.
- Activity(Activity) - Constructor for class etomica.action.Activity
-
Copy constructor.
- activity - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
-
- activity - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- ActivityGroup - Interface in etomica.action.activity
-
- ActivityGroupParallel - Class in etomica.action.activity
-
Organizer of simulation actions to be executed in parallel,
each on its own thread.
- ActivityGroupParallel() - Constructor for class etomica.action.activity.ActivityGroupParallel
-
- ActivityGroupParallel(IAction[]) - Constructor for class etomica.action.activity.ActivityGroupParallel
-
- ActivityGroupSeries - Class in etomica.action.activity
-
Organizer of simulation actions to be executed in series.
- ActivityGroupSeries() - Constructor for class etomica.action.activity.ActivityGroupSeries
-
- ActivityIntegrate - Class in etomica.action.activity
-
Activity that repeatedly invokes an Integrator's doStep method.
- ActivityIntegrate(Integrator) - Constructor for class etomica.action.activity.ActivityIntegrate
-
Constructs activity to generate configurations with
the given integrator (which is final).
- ActivityIntegrate(Integrator, int, boolean) - Constructor for class etomica.action.activity.ActivityIntegrate
-
- activityIntegrate - Variable in class etomica.AlkaneEH.CH4NVT
-
- activityIntegrate - Variable in class etomica.AlkaneEH.DHS_NVT
-
- activityIntegrate - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
-
- activityIntegrate - Variable in class etomica.densityofstate.DensityOfState
-
- activityIntegrate - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
-
- activityIntegrate - Variable in class etomica.dielectric.DHS_NVT
-
- activityIntegrate - Variable in class etomica.dielectric.DLJ_NVT_1site
-
- activityIntegrate - Variable in class etomica.dielectric.TIP4P_NVT
-
- activityIntegrate - Variable in class etomica.dimer.IntegratorDimerMin
-
- activityIntegrate - Variable in class etomica.dimer.IntegratorDimerRT
-
- activityIntegrate - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- activityIntegrate - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- activityIntegrate - Variable in class etomica.mappedRdf.MappedRdf
-
- activityIntegrate - Variable in class etomica.mappedvirial.MappedU
-
- activityIntegrate - Variable in class etomica.mappedvirial.MappedVirialLJ
-
- activityIntegrate - Variable in class etomica.mappedvirial.MappedVirialLJVGr
-
- activityIntegrate - Variable in class etomica.meam.EFSTungsten
-
- activityIntegrate - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- activityIntegrate - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- activityIntegrate - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- activityIntegrate - Variable in class etomica.meam.MEAM_MC
-
- activityIntegrate - Variable in class etomica.meam.MEAMMd3D
-
- activityIntegrate - Variable in class etomica.metastable.LJmuVT
-
- activityIntegrate - Variable in class etomica.metastable.LJNPT
-
- activityIntegrate - Variable in class etomica.metastable.LJNVT
-
- activityIntegrate - Variable in class etomica.models.hexane.HexaneVolumeFraction
-
- activityIntegrate - Variable in class etomica.models.hexane.SimHarmonicHexane
-
- activityIntegrate - Variable in class etomica.models.hexane.TestHexane
-
- activityIntegrate - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
-
- activityIntegrate - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- activityIntegrate - Variable in class etomica.models.hexane.TestHexaneHarmonic
-
- activityIntegrate - Variable in class etomica.models.hexane.TestSetToUHexane
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- activityIntegrate - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.SimWidomMode
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- activityIntegrate - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- activityIntegrate - Variable in class etomica.modules.adsorption.Adsorption
-
- activityIntegrate - Variable in class etomica.modules.catalysis.Catalysis
-
- activityIntegrate - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- activityIntegrate - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- activityIntegrate - Variable in class etomica.modules.colloid.ColloidSim
-
- activityIntegrate - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- activityIntegrate - Variable in class etomica.modules.droplet.Droplet
-
- activityIntegrate - Variable in class etomica.modules.droplet.DropletAtomic
-
- activityIntegrate - Variable in class etomica.modules.ensembles.LJMC
-
- activityIntegrate - Variable in class etomica.modules.entropylottery.EntropyLottery
-
- activityIntegrate - Variable in class etomica.modules.insertion.Insertion
-
- activityIntegrate - Variable in class etomica.modules.interfacial.InterfacialSW
-
- activityIntegrate - Variable in class etomica.modules.ljmd.Ljmd
-
- activityIntegrate - Variable in class etomica.modules.mu.Mu
-
- activityIntegrate - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- activityIntegrate - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- activityIntegrate - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- activityIntegrate - Variable in class etomica.modules.osmosis.OsmosisSim
-
- activityIntegrate - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- activityIntegrate - Variable in class etomica.modules.render.RenderMD
-
- activityIntegrate - Variable in class etomica.modules.rheology.SimulationRheology
-
- activityIntegrate - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- activityIntegrate - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- activityIntegrate - Variable in class etomica.modules.sam.Sam
-
- activityIntegrate - Variable in class etomica.modules.swmd.Swmd
-
- activityIntegrate - Variable in class etomica.modules.vle.VLESim
-
- activityIntegrate - Variable in class etomica.normalmode.HessianDB
-
- activityIntegrate - Variable in class etomica.normalmode.HSDimerNPT
-
- activityIntegrate - Variable in class etomica.normalmode.HSNPT
-
- activityIntegrate - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- activityIntegrate - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- activityIntegrate - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- activityIntegrate - Variable in class etomica.normalmode.SimBennet
-
- activityIntegrate - Variable in class etomica.normalmode.SimCalcJ
-
- activityIntegrate - Variable in class etomica.normalmode.SimCalcS
-
- activityIntegrate - Variable in class etomica.normalmode.SimCalcSLJ
-
- activityIntegrate - Variable in class etomica.normalmode.SimCalcSMorse
-
- activityIntegrate - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
-
- activityIntegrate - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- activityIntegrate - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- activityIntegrate - Variable in class etomica.normalmode.SimEinStep1
-
- activityIntegrate - Variable in class etomica.normalmode.SimEinStep1HCP
-
- activityIntegrate - Variable in class etomica.normalmode.SimEinStep2
-
- activityIntegrate - Variable in class etomica.normalmode.SimEinStep2HCP
-
- activityIntegrate - Variable in class etomica.normalmode.SimFluidSoftSphere
-
- activityIntegrate - Variable in class etomica.normalmode.SimHarmonic
-
- activityIntegrate - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- activityIntegrate - Variable in class etomica.normalmode.SimLJHTTISuper
-
- activityIntegrate - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- activityIntegrate - Variable in class etomica.normalmode.SimModesJ
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlap
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapLJ
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapLJModule
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapModule
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- activityIntegrate - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- activityIntegrate - Variable in class etomica.normalmode.SimTarget
-
- activityIntegrate - Variable in class etomica.normalmode.SimTargetUmbrella
-
- activityIntegrate - Variable in class etomica.normalmode.SimUmbrella
-
- activityIntegrate - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- activityIntegrate - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- activityIntegrate - Variable in class etomica.surfacetension.LJMC
-
- activityIntegrate - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- activityIntegrate - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- activityIntegrate - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- activityIntegrate - Variable in class etomica.zeolite.ZeoliteSimulation
-
- activityIntegrateDimer - Variable in class etomica.dimer.SimDimerLJadatom
-
- activityIntegrateDimer - Variable in class etomica.dimer.SimDimerLJgb
-
- activityIntegrateDimer - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- activityIntegrateDimer - Variable in class etomica.dimer.SimDimerMEAMGB
-
- activityIntegrateDimer - Variable in class etomica.kmc.SimKMCLJadatom
-
- activityIntegrateDimer - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- activityIntegrateKMC - Variable in class etomica.kmc.SimKMCLJadatom
-
- activityIntegrateKMC - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- activityIntegrateKMCCluster - Variable in class etomica.kmc.SimKMCLJadatom
-
- activityIntegrateKMCCluster - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- activityIntegrateMAP - Variable in class etomica.dimer.EnergyMap
-
- activityIntegrateMD - Variable in class etomica.dimer.SimDimerLJadatom
-
- activityIntegrateMD - Variable in class etomica.dimer.SimDimerLJgb
-
- activityIntegrateMD - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- activityIntegrateMD - Variable in class etomica.dimer.SimDimerMEAMGB
-
- activityIntegrateMin - Variable in class etomica.dimer.SimDimerLJadatom
-
- activityIntegrateMin - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- activityIntegrateMin - Variable in class etomica.dimer.SimDimerMEAMGB
-
- actualFlipList - Variable in class etomica.virial.ClusterCoupledFlippedPartial
-
- acType - Variable in class etomica.models.rowley.SpeciesEthanol
-
- acType - Variable in class etomica.models.rowley.SpeciesMethanol
-
- adAtomPos - Variable in class etomica.dimer.SimDimerLJadatom
-
- adAtomPos - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- adAtomPos - Variable in class etomica.dimer.SimDimerMEAMGB
-
- adAtomPos - Variable in class etomica.kmc.SimKMCLJadatom
-
- adAtomPos - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- add(IAtom) - Method in class etomica.atom.AtomArrayList
-
- add(Feature) - Method in class etomica.compatibility.FeatureSet
-
- add(String, String) - Method in class etomica.compatibility.FeatureSet
-
- add(String, double) - Method in class etomica.compatibility.FeatureSet
-
- add(Requirement) - Method in class etomica.compatibility.RequirementSet
-
- add(Coefficient) - Method in interface etomica.graph.model.Coefficient
-
- add(E) - Method in class etomica.graph.model.GraphList
-
- add(Coefficient) - Method in class etomica.graph.model.impl.CoefficientImpl
-
- add(Display) - Method in class etomica.graphics.SimulationGraphic
-
- add(Device) - Method in class etomica.graphics.SimulationGraphic
-
Adds displays graphic to the simulation display pane
- add(IFunction) - Method in class etomica.math.function.FunctionChain
-
Adds the given function to the chain of functions.
- add(IMolecule) - Method in class etomica.molecule.MoleculeArrayList
-
- add(P2HardBondedList.MyBond) - Method in class etomica.potential.P2HardBondedList.BondArrayList
-
- add(TreeLinker) - Method in class etomica.util.TreeList
-
- add(BigDecimal, BigInteger) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Add a BigDecimal and a BigInteger.
- add(BigIntegerPoly) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Add another polynomial
- add(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurd
-
Add two surds of compatible discriminant.
- add(BigSurdVec) - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Add two vectors algebraically.
- add(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Add two vectors algebraically.
- add(BigInteger) - Method in class etomica.veos.bigdecimal.Ifactor
-
Summation with another positive integer
- add(Rational) - Method in class etomica.veos.bigdecimal.Rational
-
Add another fraction.
- add(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
Add another integer.
- add(int) - Method in class etomica.veos.bigdecimal.Rational
-
Add another integer.
- add(Matrix3f) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to sum of itself and matrix m1.
- add(float) - Method in class org.jmol.util.Quaternion
-
- add(Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the vector sum of itself and tuple t1.
- add(Tuple3i) - Method in class org.jmol.util.Tuple3i
-
Sets the value of this tuple to the sum of itself and t1.
- add2(Tuple3f, Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the vector sum of tuples t1 and t2.
- ADD_HYDROGEN_TITLE - Static variable in class org.jmol.viewer.JmolConstants
-
- addAccumulator(ConstructionParams, String, String) - Method in class etomica.server.resources.data.DataStreamResource
-
- addAction(IAction) - Method in interface etomica.action.ActionGroup
-
Adds the given action to this group, placing it at the end of the list.
- addAction(IAction) - Method in class etomica.action.ActionGroupSeries
-
- addAction(IAction) - Method in class etomica.action.activity.ActivityGroupParallel
-
- addAction(IAction) - Method in class etomica.action.activity.ActivityGroupSeries
-
Adds the given action to the list of actions.
- addAction(IAction) - Method in class etomica.action.activity.Controller
-
- addAddSpecies1ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addAddSpecies2ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addAddSpecies3ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addAlkaneLengthViewListener(int) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- addAll(IAtomList) - Method in class etomica.atom.AtomArrayList
-
- addAll(Collection<? extends E>) - Method in class etomica.graph.model.GraphList
-
- addAll(IMoleculeList) - Method in class etomica.molecule.MoleculeArrayList
-
- addAlterSimEnvButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addAlterSimEnvButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addAnotherSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addAsTab(Component, String, boolean) - Method in class etomica.graphics.SimulationGraphic
-
- addAtom(IAtom) - Method in class etomica.nbr.cell.Cell
-
- addAtomNotify(IAtom) - Method in class etomica.nbr.list.NeighborListManager
-
Constructs neighbor lists for the given atom
- addAtomNotify(IAtom) - Method in class etomica.nbr.list.NeighborListManagerSlanty
-
Constructs neighbor lists for the given atom
- addAuthor(String) - Method in class etomica.graphics.DefaultToolbar
-
- addBDOne(BigDecimal) - Static method in class etomica.data.types.DataDoubleBDArray
-
- addBDZero(BigDecimal) - Static method in class etomica.data.types.DataDoubleBDArray
-
- addBondedPotentialSets(CollectionPotentialAtomicLike, Space, int) - Method in class etomica.virial.GUI.components.ACollectionBondedPotential
-
- addBondedPotentialSets(CollectionPotentialAtomicLike, Space, int) - Method in class etomica.virial.GUI.components.CollectionBondedPotentialAlcohols
-
- addBondedPotentialSets(CollectionPotentialAtomicLike, Space, int) - Method in class etomica.virial.GUI.components.CollectionBondedPotentialAlkanes
-
- addBoundBoxPoint(Point3f) - Method in class org.jmol.util.BoxInfo
-
- addBox(Box) - Method in class etomica.simulation.Simulation
-
Adds a Box to the simulation.
- addButton(String, IAction) - Method in class etomica.graphics.DeviceButtonGroup
-
Adds a radio button with the given label, which (when selected) performs
the given action.
- addCellNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Add the specified listener to the list of listeners that
will get invoked when the 'nCell #' slider value changes.
- addChangeableWV(int[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- addChangeableWV(String) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- addChildAtom(IAtom) - Method in class etomica.molecule.Molecule
-
Adds the given Atom as a child of this Atom.
- addChildType(AtomType) - Method in class etomica.species.Species
-
- addChildType(AtomType) - Method in class etomica.species.SpeciesSpheresHetero
-
Adds the given factory as a child of this factory.
- addChooseOkayButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- addCloseWindowButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlertMsgBox
-
- addCloseWindowButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- addCloseWindowButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- addCluster(ClusterDiagram) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
-
- addClusterDiagram(ClusterDiagram) - Method in class etomica.virial.cluster.ClusterDiagramTree
-
Adds the given diagram to the tree, adding nodes as needed
- addCollisionListener(IntegratorHard.CollisionListener) - Method in class etomica.integrator.IntegratorHard
-
Registers an object that implements the CollisionListener interface.
- addComparator(Comparator<Graph>) - Method in class etomica.graph.model.comparators.ComparatorChain
-
Add a comparator that will be used to sort sort graphs.
- addComponent(Component, JPanel, int, int, int, int) - Method in class etomica.modules.clustergenerator.MyApplet
-
Componet c is added to JPanel panel following the rule of GridBagLayout manager
- addConnection(int, int) - Method in class etomica.virial.cluster.ClusterDiagram
-
Adds a connection between the node1 and node2.
- addContributor(String) - Method in class etomica.graphics.DefaultToolbar
-
- addCountOfSpeciesSLMListener(ChangeListener, int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addData(IData) - Method in class etomica.data.AccumulatorAverageBlockless
-
Add the given values to the sums and block sums.
- addData(IData) - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
Add the given values to the sums and block sums.
- addData(IData) - Method in class etomica.data.AccumulatorAverageBootstrap
-
Add the given values to the sums and block sums.
- addData(IData) - Method in class etomica.data.AccumulatorAverageCollapsing
-
Add the given values to the sums and block sums.
- addData(IData) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Add the given values to the sums and block sums.
- addData(IData) - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
-
Add the given values to the sums and block sums.
- addData(IData) - Method in class etomica.data.AccumulatorAverageCovariance
-
- addData(IData) - Method in class etomica.data.AccumulatorAverageFixed
-
Add the given values to the sums and block sums.
- addData(IData) - Method in class etomica.data.AccumulatorAverageFixedOutputFile
-
Add the given values to the sums and block sums.
- addData(IData) - Method in class etomica.data.AccumulatorCounter
-
Increments the counter.
- addData(IData) - Method in class etomica.data.AccumulatorHistogram
-
Adds each value in the given Data to its own histogram.
- addData(IData) - Method in class etomica.data.AccumulatorHistory
-
Adds each value in the given array to its own history.
- addData(IData) - Method in class etomica.data.DataAccumulator
-
Defined by subclass to specify what this accumulator does when data is added to it.
- addData(BigDecimal, MathContext) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- addData(double) - Method in class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- addData(double[]) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- addData(double[]) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyDataCov
-
- addData(IData) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
Add the given values to the sums and block sums
- addDataListener(DataSetListener) - Method in class etomica.data.DataSet
-
- addDataSink(IDataSink, AccumulatorAverage.StatType[]) - Method in class etomica.data.AccumulatorAverage
-
Adds a new DataSink that will receive a specific subset of the statistics
generated by this accumulator.
- addDataSink(IDataSink, AccumulatorAverageBlockless.StatType[]) - Method in class etomica.data.AccumulatorAverageBlockless
-
Adds a new DataSink that will receive a specific subset of the statistics
generated by this accumulator.
- addDataSink(IDataSink) - Method in class etomica.data.DataFork
-
- addDataSink(IDataSink) - Method in interface etomica.data.DataPipeForked
-
Adds the given DataSink to those receiving the Data entering this DataFork,
keeping all previously entered DataSinks.
- addDataSink(IDataSink) - Method in class etomica.data.DataProcessorForked
-
Adds the given DataSink to those receiving the Data entering this DataFork,
keeping all previously entered DataSinks.
- addDataSource(IDataSource) - Method in class etomica.data.DataSourceGroup
-
Adds the given DataSource to those held by the group.
- addDataSource(IDataSource) - Method in class etomica.data.DataTableAverages
-
Adds the given data source to those feeding the table.
- addDownNbr(IAtom, int) - Method in class etomica.nbr.list.AtomNeighborLists
-
Adds the given atom as a "down" neighbor interacting via the potential
with the given index.
- addDownNbr(IMolecule, int) - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists
-
Adds the given atom as a "down" neighbor interacting via the potential
with the given index.
- addDrawable(Drawable) - Method in class etomica.graphics.DisplayBox
-
- addDrawable(Object) - Method in class etomica.graphics.DisplayBox
-
- addEditVariablesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addEditVariablesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addEquivalents(ArrayList<ClusterDiagram>) - Static method in class etomica.virial.cluster.ClusterOperations
-
Replaces all isomorphic clusters in the given list by a single cluster
with weight given by their sum.
- addEValNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Add the specified listener to the list of listeners that
will get invoked when the 'eigenvalues #' slider value changes.
- addFactors(int[]) - Method in interface etomica.graph.model.Graph
-
- addFactors(int[]) - Method in class etomica.graph.model.impl.GraphImpl
-
- addFig(Figure) - Method in class g3dsys.control.G3DSys
-
Adds the Figure to the associated FigureManager
- addFilter(String) - Method in class etomica.graph.engine.impl.ConstructorImpl
-
- addFilter(String) - Method in interface etomica.graph.engine.Parser.Constructor
-
- addIntegrator(Integrator) - Method in class etomica.integrator.IntegratorGEMC
-
- addIntegrator(Integrator) - Method in class etomica.integrator.IntegratorManagerMC
-
- addIntegrator(IntegratorBox) - Method in class etomica.integrator.IntegratorPT
-
Adds the given integrator to those managed by this integrator, and
includes integrator's box to the set among which configurations are
swapped.
- addIntersectionVertex(Point3f, float, int, int, Map<String, Integer>, int, int) - Method in class org.jmol.util.MeshSurface
-
- additive - Variable in class etomica.virial.simulations.VirialGCPM.VirialGCPMParam
-
- addLine(LineSegment) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- addListener(BoxEventListener) - Method in class etomica.box.BoxEventManager
-
- addListener(IntegratorListener) - Method in class etomica.integrator.IntegratorEventManager
-
Adds the given listener to this event manager.
- addListener(IntegratorListener) - Method in class etomica.integrator.IntegratorListenerGroupSeries
-
Adds the given listener to the group.
- addListener(INeighborListListenerMolecular) - Method in class etomica.nbr.list.molecule.NeighborListEventManagerMolecular
-
- addListener(INeighborListListener) - Method in class etomica.nbr.list.NeighborListEventManager
-
- addListener(SimulationListener) - Method in class etomica.simulation.SimulationEventManager
-
- addListener(BoundaryEventListener) - Method in class etomica.space.BoundaryEventManager
-
Adds the given listener to this event manager.
- addListener(IListener<E>) - Method in class etomica.util.EventManager
-
Adds the given listener to this event manager.
- addMCMove(MCMove) - Method in class etomica.integrator.mcmove.MCMoveManager
-
Adds the given MCMove to the set of moves performed by the integrator and
recalculates move frequencies.
- addModel(Model) - Method in class etomica.graphics.BondListener
-
Infroms the BondListener that is should track bonds associated with all
molecules of the given Model.
- addModel(Model) - Method in class etomica.potential.PotentialMaster
-
Add the given Model's intramolecular potentials to this PotentialMaster
- addMolecule(IMolecule) - Method in class etomica.box.Box
-
Adds the given molecule to the this Box.
- addMolecule(IMolecule) - Method in class etomica.nbr.cell.molecule.CellMolecular
-
- addMoleculeListDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addMoleculeListDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addMoleculeNotify(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
Constructs neighbor lists for the given atom
- addMoleculeNotify(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular
-
Constructs neighbor lists for the given molecule
- addNewMolecule(ISpecies) - Method in class etomica.box.Box
-
Creates a molecule of the given species and adds it to the box
- addNoDoNotRemoveSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
-
- addObject(T[], T) - Static method in class etomica.util.Arrays
-
Returns an array formed from adding the newObject to the elements
in the given array.
- addOption(String, IAction) - Method in class etomica.graphics.DeviceSelector
-
- addPair(NodePair) - Method in interface etomica.graph.isomorphism.SearchState
-
- addPair(NodePair) - Method in class etomica.graph.isomorphism.UllmanSearchState
-
- addPair(NodePair) - Method in class etomica.graph.isomorphism.VF2SearchState
-
- addPair(NodePair) - Method in class etomica.graph.isomorphism.VFSearchState
-
- addParser(ParameterParser) - Method in class etomica.util.ParameterBase
-
- addPlane(Plane) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- addPoint(Point3f, Point3f, Point3f, float) - Static method in class org.jmol.util.BoxInfo
-
- addPointXYZ(float, float, float, Point3f, Point3f, float) - Static method in class org.jmol.util.BoxInfo
-
- addPolygonC(int[], int, BitSet) - Method in class org.jmol.util.MeshSurface
-
- addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- addPotential(IPotentialAtomic, AtomsetIteratorBasisDependent, AtomType[]) - Method in class etomica.nbr.PotentialGroupNbr
-
- addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.PotentialMasterHybrid
-
- addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.PotentialMasterNbr
-
- addPotential(IPotential) - Method in class etomica.potential.PotentialArray
-
Identifies the given potential to this type instance and returns
the index assigned to it.
- addPotential(IPotential, AtomType) - Method in class etomica.potential.PotentialArrayByType
-
Identifies the given potential to this type instance and returns
the index assigned to it.
- addPotential(IPotentialMolecular) - Method in class etomica.potential.PotentialArrayMolecular
-
Identifies the given potential to this type instance and returns
the index assigned to it.
- addPotential(IPotentialAtomic, AtomType[]) - Method in class etomica.potential.PotentialGroup
-
Adds the given potential and sets it up to apply to the atoms in the basis
having the given types.
- addPotential(IPotentialAtomic, AtomsetIteratorBasisDependent) - Method in class etomica.potential.PotentialGroup
-
Adds the given potential to this group, defining it to apply to the atoms
provided by the given basis-dependent iterator.
- addPotential(IPotentialAtomic, AtomsetIteratorBasisDependent, AtomType[]) - Method in class etomica.potential.PotentialGroup
-
- addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.potential.PotentialMaster
-
Indicates to the PotentialMaster that the given potential should apply to
the specified species.
- addPotential(IPotentialAtomic, AtomType[]) - Method in class etomica.potential.PotentialMaster
-
Indicates to the PotentialMaster that the given potential should apply to
the specified atom types.
- addPotential(IPotentialMolecular, MoleculesetIteratorPDT, ISpecies[]) - Method in class etomica.potential.PotentialMaster
-
- addPotential(IPotentialMolecular) - Method in class etomica.potential.PotentialMasterLrc
-
- addPotential(IPotentialAtomic) - Method in class etomica.potential.PotentialMasterLrc
-
- addPotential(IPotentialMolecular, ISpecies[]) - Method in class etomica.potential.PotentialMasterMonatomic
-
- addPotential(IPotentialAtomic, AtomType[]) - Method in class etomica.potential.PotentialMasterMonatomic
-
- addPotentialButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addPotentialButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addPotentialNbrList(IPotentialAtomic, AtomType[], NeighborCriterion) - Method in class etomica.nbr.list.PotentialMasterList
-
Add the given potential to be used for the given atom types and the
given criterion.
- addPotentialsJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addPotentialsJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addPotParamDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addPotParamDisplayLSMListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addPotParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addPotParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addProgressListener(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
Causes a progress report (coefficient value and uncertainty) 10 times
during the course of the simulation.
- addProgressListener(double, boolean) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
Causes a progress report (coefficient value and uncertainty) 10 times
during the course of the simulation.
- addPropertyChangeListener(PropertyChangeListener) - Method in class etomica.graphics.Display
-
- addPropertyChangeListener(PropertyChangeListener) - Method in class etomica.util.Grabber.ActionCornerSetter
-
- addQuad(int, int, int, int) - Method in class org.jmol.util.MeshSurface
-
- addRadioGroupActionListener(ActionListener) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Add the specified listener to the list of listeners that
will get invoked when the isothermal or adiabatic radio button
is pushed.
- addRadioGroupActionListener(ActionListener) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Add the specified listener to the list of listeners that
will get invoked when the "x-axis" or "y-axis" radio button
is pushed.
- addRadioGroupActionListener(ActionListener) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Add the specified listener to the list of listeners that
will get invoked when the "Eigenvalue" or "All Eigenvalues" radio button
is pushed.
- addRadioGroupActionListener(ActionListener) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Add the specified listener to the list of listeners that
will get invoked when the "Wave Vector" or "All Wave Vectors" radio button
is pushed.
- addRangedPotential(IPotentialMolecular, ISpecies) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- addRangedPotential(IPotentialAtomic, AtomType) - Method in class etomica.nbr.PotentialMasterNbr
-
- addRangedPotentialForSpecies(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Adds the potential as a ranged potential that applies to the given
AtomTypes.
- addRangedPotentialForSpecies(IPotentialMolecular, ISpecies[]) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- addRangedPotentialForTypes(IPotentialAtomic, AtomType[]) - Method in class etomica.nbr.list.PotentialMasterList
-
Adds the potential as a ranged potential that applies to the given
AtomTypes.
- addRangedPotentialForTypes(IPotentialAtomic, AtomType[]) - Method in class etomica.nbr.PotentialMasterHybrid
-
- addRangedPotentialForTypes(IPotentialAtomic, AtomType[]) - Method in class etomica.nbr.PotentialMasterNbr
-
- addRangedPotentialForTypes(IPotentialAtomic, AtomType[]) - Method in class etomica.nbr.site.PotentialMasterSite
-
- addRemoveButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addRemoveSpecies1ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addRemoveSpecies2ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addRemoveSpecies3ButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addResetButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addResetButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addReverseComparator(Comparator<Graph>) - Method in class etomica.graph.model.comparators.ComparatorChain
-
Add a comparator that will be used to sort sort graphs in reverse order.
- addRound(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Add and round according to the larger of the two ulp's.
- addRound(BigComplex, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Add and round according to the larger of the two ulp's.
- addRound(BigComplex, BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Add and round according to the larger of the two ulp's.
- addRunButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addRunButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addSameSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addSaveValuesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- addSaveValuesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- addSpecies(ISpecies) - Method in class etomica.config.ConfigurationLatticeWithPlane
-
- addSpecies(ISpecies) - Method in class etomica.simulation.Simulation
-
Adds species to the list of all ISpecies in the simulation, and
notifies all Boxes of the addition.
- addSpecies(Object) - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
-
- addSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addSpeciesIndextoSites(String[], int) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- addSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- addSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- addSpeciesMolecule(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- addSpeciesNotify(ISpecies) - Method in class etomica.box.Box
-
Notifies the Box that the given species has been added to the
simulation.
- addStateChangedListener(ChangeListener) - Method in class etomica.modules.osmosis.Osmosis.InitializeMolecules
-
- addTag(DataTag) - Method in class etomica.data.DataInfo
-
Adds the tag
- addTag(DataTag) - Method in interface etomica.data.IDataInfo
-
Adds the tag to this IDataInfo object.
- addTag(DataTag) - Method in class etomica.data.types.DataGroup.DataInfoGroup
-
- addTags(DataTag[]) - Method in class etomica.data.DataInfo
-
Convenience method to add all of the given tags.
- addTags(DataTag[]) - Method in interface etomica.data.IDataInfo
-
Convenience method to add all of the given tags.
- addTags(DataTag[]) - Method in class etomica.data.types.DataGroup.DataInfoGroup
-
- addTemperatureSliderListener(ChangeListener) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Add the specified listener to the list of listeners that
will get invoked when the temperature slider value changes.
- addTensor(int, Tensor) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
Adds the given contribution to the virial sum for bin iBin.
- addThermostatAction(IAction) - Method in class etomica.normalmode.IntegratorHardMDMC
-
- addToHashMapPotentialNonBonded(String[], IPotential) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- addToHashMapPotentialNonBonded(String[], IPotential) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- addToken(String, Token) - Static method in class org.jmol.script.Token
-
- addTriangle(int, int, int) - Method in class org.jmol.util.MeshSurface
-
- addTriangleCheck(int, int, int, int, int, int) - Method in class org.jmol.util.MeshSurface
-
- addUpNbr(IAtom, int) - Method in class etomica.nbr.list.AtomNeighborLists
-
Adds the given atom as a "down" neighbor interacting via the potential
with the given index.
- addUpNbr(IMolecule, int) - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists
-
Adds the given atom as a "down" neighbor interacting via the potential
with the given index.
- addValue(double) - Method in interface etomica.data.histogram.Histogram
-
Adds the given value to the Histogram
- addValue(double) - Method in class etomica.data.histogram.HistogramCollapsing
-
- addValue(double) - Method in class etomica.data.histogram.HistogramDiscrete
-
- addValue(double) - Method in class etomica.data.histogram.HistogramExpanding
-
- addValue(double, double) - Method in class etomica.data.histogram.HistogramNotSoSimple
-
- addValue(double) - Method in class etomica.data.histogram.HistogramNotSoSimple
-
- addValue(double, double) - Method in class etomica.data.histogram.HistogramReweightedData
-
- addValue(double) - Method in class etomica.data.histogram.HistogramReweightedData
-
- addValue(double) - Method in class etomica.data.histogram.HistogramSimple
-
- addValue(double, double) - Method in interface etomica.data.history.History
-
Adds the given x, y pair to the History.
- addValue(double, double) - Method in class etomica.data.history.HistoryCollapsingAverage
-
adds data to the history.
- addValue(double, double) - Method in class etomica.data.history.HistoryCollapsingDiscard
-
adds data to the history.
- addValue(double, double) - Method in class etomica.data.history.HistoryComplete
-
- addValue(double, double) - Method in class etomica.data.history.HistoryScrolling
-
- addValueChangedListener(DeviceBoxValueChangedListener) - Method in class etomica.graphics.DeviceBox
-
Add an object to be notified when the DeviceBox value to changes
- addVertexCopy(Point3f) - Method in class org.jmol.util.MeshSurface
-
- addVertexCopy(Point3f, float, boolean, int) - Method in class org.jmol.util.MeshSurface
-
- addVertexCopyVal(Point3f, float) - Method in class org.jmol.util.MeshSurface
-
- addWaveVectorNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Add the specified listener to the list of listeners that
will get invoked when the 'wave vectors #' slider value changes.
- addXYCellNumSliderListener(ChangeListener) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Add the specified listener to the list of listeners that
will get invoked when the 'xCell #' and 'yCell #' slider value changes.
- addYesRemoveSpeciesButtonListener(ActionListener) - Method in class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
-
- aDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- aDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- aDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- adjustCountdown - Variable in class etomica.overlap.IntegratorOverlap
-
- adjustInterval - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
-
- adjustInterval - Variable in class etomica.overlap.IntegratorOverlap
-
- adjustStep - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
-
- adjustStepFreq() - Method in class etomica.virial.overlap.IntegratorOverlap
-
Adjusts the frequency with which steps for each sub-integrator are
performed.
- adjustStepFreq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- adjustStepFreq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- adjustStepFrequency - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
-
- adjustStepFrequency - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- adjustStepFrequency - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- adjustStepSize() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
- adpmax - Static variable in class org.jmol.script.Token
-
- adpmin - Static variable in class org.jmol.script.Token
-
- Adsorption - Class in etomica.modules.adsorption
-
Simulation for Adsorption module.
- Adsorption(Space) - Constructor for class etomica.modules.adsorption.Adsorption
-
- AdsorptionGraphic - Class in etomica.modules.adsorption
-
Catalysis graphical app.
- AdsorptionGraphic(Adsorption, Space) - Constructor for class etomica.modules.adsorption.AdsorptionGraphic
-
- AdsorptionGraphic.Applet - Class in etomica.modules.adsorption
-
- advance() - Method in class etomica.graph.iterators.CartesianIterator
-
- advance() - Method in class etomica.graph.iterators.CartesianPermutator
-
- advance() - Method in class etomica.virial.cluster.ClusterGenerator
-
Advances the cluster to the next cluster matching the given criteria.
- advanceAcrossTimeStep(double) - Method in class etomica.integrator.IntegratorHard
-
Advances all atom coordinates by tStep, without any intervening collisions.
- advanceAcrossTimeStep(double) - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
-
- advanceAcrossTimeStep(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- advanceParameters() - Method in class etomica.thermointegration.IntegratorThermodynamic
-
Method to advance the thermodynamic parameter(s) of interest as part
of the thermodynamic integration.
- advanceParameters() - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- aEE - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- aEE - Variable in class etomica.dielectric.TIP4P_NVT.Param
-
- Aelement - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- aErr - Variable in class etomica.potential.P2HePCKLJS
-
- affectedAtomIterator - Variable in class etomica.association.MCMoveDimer
-
- affectedAtomIterator - Variable in class etomica.association.MCMoveDimerRotate
-
- affectedAtomIterator - Variable in class etomica.association.MCMoveSmer
-
- affectedAtomIterator - Variable in class etomica.association.MCMoveSmerRotate
-
- affectedAtomIterator - Variable in class etomica.association.MCMoveVolumeAssociated
-
- affectedAtomIterator - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- affectedAtomIterator - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- affectedAtomIterator - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveAtom
-
- affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
-
- affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- affectedAtomIterator - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- affectedAtomIterator - Variable in class etomica.models.nitrogen.MCMoveVolumeN2
-
- affectedAtomIterator - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- affectedAtomIterator - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeSolid
-
- affectedAtomIterator - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- affectedAtomIterator - Variable in class etomica.spin.MCMoveSpinFlip
-
- affectedAtomIterator - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- affectedAtomIterator - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- affectedAtomList - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- affectedAtoms() - Method in class etomica.association.MCMoveBiasUB
-
- affectedAtoms() - Method in class etomica.association.MCMoveBiasUBMolecule
-
- affectedAtoms - Variable in class etomica.association.MCMoveDimer
-
- affectedAtoms() - Method in class etomica.association.MCMoveDimer
-
- affectedAtoms - Variable in class etomica.association.MCMoveDimerRotate
-
- affectedAtoms() - Method in class etomica.association.MCMoveDimerRotate
-
- affectedAtoms() - Method in class etomica.association.MCMoveSmer
-
- affectedAtoms() - Method in class etomica.association.MCMoveSmerRotate
-
- affectedAtoms() - Method in class etomica.association.MCMoveVolumeAssociated
-
- affectedAtoms() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- affectedAtoms() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- affectedAtoms() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- affectedAtoms() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- affectedAtoms(Box) - Method in class etomica.integrator.mcmove.MCMove
-
Returns an iterator that yields the atoms that were affected by the trial
move the last time doTrial was invoked (regardless of whether the move
was accepted).
- affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveAtom
-
- affectedAtoms(Box) - Method in class etomica.integrator.mcmove.MCMoveBox
-
- affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveBox
-
- affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
-
- affectedAtoms - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveDimer
-
- affectedAtoms - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
Returns an iterator giving molecule that is being added or deleted
in the current or most recent trial.
- affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
- affectedAtoms(Box) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
- affectedAtoms(Box) - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
-
- affectedAtoms() - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- affectedAtoms(Box) - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
-
- affectedAtoms() - Method in class etomica.models.hexane.MCMoveCBMC
-
- affectedAtoms() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- affectedAtoms() - Method in class etomica.models.hexane.MCMoveReptate
-
- affectedAtoms() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- affectedAtoms() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- affectedAtoms() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- affectedAtoms() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- affectedAtoms() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- affectedAtoms() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- affectedAtoms() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- affectedAtoms() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveAtomSuperBox
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveHarmonic
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveHarmonicStep
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
- affectedAtoms() - Method in class etomica.normalmode.MCMovePhaseAngle
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveSingleMode
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- affectedAtoms() - Method in class etomica.normalmode.MCMoveWV
-
- affectedAtoms() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- affectedAtoms() - Method in class etomica.spin.MCMoveSpinFlip
-
- affectedAtoms() - Method in class etomica.virial.MCMoveChangeBondLength
-
- affectedAtoms() - Method in class etomica.virial.MCMoveClusterAngleBend
-
- affectedAtoms() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- affectedAtoms() - Method in class etomica.virial.MCMoveClusterAtomQ
-
- affectedAtoms(Box) - Method in class etomica.virial.MCMoveClusterAtomQ
-
- affectedAtoms() - Method in class etomica.virial.MCMoveClusterDiagram
-
- affectedAtoms() - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingRegrow
-
- affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- affectedAtoms() - Method in class etomica.virial.MCMoveClusterRingScale
-
- affectedAtoms(Box) - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
-
- affectedMol - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- affectedMoleculeIterator - Variable in class etomica.association.MCMoveBiasUBMolecule
-
- affectedMoleculeIterator - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- affectedMoleculeIterator - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- affectedMoleculeIterator - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- affectedMoleculeIterator - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- affectedMoleculeIterator - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- affectedMoleculeIterator - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- affectedMoleculeList - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- affectedMoleculeList - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- affectedMoleculeList - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- affectedMoleculeList - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- affectedMoleculeList - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- affectedMolecules(Box) - Method in class etomica.association.MCMoveBiasUBMolecule
-
- affectedMolecules(Box) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- affectedMolecules(Box) - Method in interface etomica.integrator.mcmove.MCMoveMolecular
-
- affectedMolecules(Box) - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
- affectedMolecules(Box) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- affectedMolecules(Box) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- affectedWV - Variable in class etomica.models.oneDHardRods.MeterWidomMode
-
- affectedWV - Variable in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- affectedWV - Variable in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- ag - Variable in class etomica.meam.MEAM_MC
-
- ag - Variable in class etomica.meam.MEAMMd3D
-
- Ag - Static variable in class etomica.meam.ParameterSetMEAM
-
- ag - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- Ag3Sn - Static variable in class etomica.meam.ParameterSetMEAM
-
- agB - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- Agent() - Constructor for class etomica.association.MCMoveVolumeAssociated.Agent
-
- Agent() - Constructor for class etomica.association.MCMoveVolumeAssociatedMolecule.Agent
-
- Agent(Space) - Constructor for class etomica.integrator.IntegratorConNVT.Agent
-
- Agent(Space) - Constructor for class etomica.integrator.IntegratorGear4.Agent
-
- Agent(IAtom, IntegratorHard) - Constructor for class etomica.integrator.IntegratorHard.Agent
-
- Agent(Space) - Constructor for class etomica.integrator.IntegratorVerlet.Agent
-
- agentManager - Variable in class etomica.action.ActionMinimizeEnergy
-
- agentManager - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
-
- agentManager - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- agentManager - Variable in class etomica.graphics.ColorSchemeCollectiveAgent
-
- agentManager - Variable in class etomica.integrator.IntegratorConNVT
-
- agentManager - Variable in class etomica.integrator.IntegratorGear4
-
- agentManager - Variable in class etomica.integrator.IntegratorHard
-
- agentManager - Variable in class etomica.integrator.IntegratorVelocityVerlet
-
- agentManager - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- agentManager - Variable in class etomica.integrator.IntegratorVerlet
-
- agentManager - Variable in class etomica.interfacial.FixedWall
-
- agentManager - Variable in class etomica.modules.catalysis.ColorSchemeRadical
-
- agentManager - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- agentManager - Variable in class etomica.modules.catalysis.InteractionTracker
-
- agentManager - Variable in class etomica.modules.catalysis.P2SquareWellBonding
-
- agentManager - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- agentManager - Variable in class etomica.modules.catalysis.P2SquareWellSurface
-
- agentManager - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- agentManager - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- agentManager - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- agentManager - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- agentManager - Variable in class etomica.modules.chainequilibrium.MeterChainLength
-
- agentManager - Variable in class etomica.modules.chainequilibrium.MeterConversion
-
- agentManager - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
- agentManager - Variable in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
- agentManager - Variable in class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- agentManager - Variable in class etomica.modules.droplet.IntegratorDroplet
-
- agentManager - Variable in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- agentManager - Variable in class etomica.modules.reactionequilibrium.P2SquareWellBonded
-
- agentManager - Variable in class etomica.modules.rosmosis.MeterFlux
-
- agentManager - Variable in class etomica.modules.rosmosis.P1Tether
-
- agentManager - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- agentManager - Variable in class etomica.nbr.cell.NeighborCellManager
-
- agentManager - Variable in class etomica.nbr.CriterionPositionWall
-
- agentManager - Variable in class etomica.nbr.CriterionSimple
-
- agentManager - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- agentManager - Variable in class etomica.normalmode.HSNPT.ActionSummer
-
- agentManager - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- agentManager1Body - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- agentManager1Body - Variable in class etomica.nbr.list.NeighborListManager
-
- agentManager2Body - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- agentManager2Body - Variable in class etomica.nbr.list.NeighborListManager
-
- agents - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- agents - Variable in class etomica.potential.P2SemiclassicalAtomic
-
- agentStream() - Method in class etomica.molecule.MoleculeAgentManager
-
- agFixedB - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- AHarm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- AHarm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- AHarm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- ahType - Variable in class etomica.models.rowley.SpeciesEthanol
-
- ahType - Variable in class etomica.models.rowley.SpeciesMethanol
-
- ai - Variable in class etomica.freeenergy.npath.SimFe
-
- ai - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- ai - Variable in class etomica.freeenergy.npath.SimLJ
-
- ai - Variable in class etomica.graphics.DeviceDelaySlider
-
- ai - Variable in class etomica.interfacial.LJMC
-
- ai - Variable in class etomica.interfacial.LJMD
-
- ai - Variable in class etomica.liquidLJ.LjMC3D
-
- ai - Variable in class etomica.liquidLJ.LjMd3D
-
- ai - Variable in class etomica.modules.pistoncylinder.PistonCylinder
-
- ai - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- ai - Variable in class etomica.normalmode.SimHSMDVacancy
-
- ai - Variable in class etomica.normalmode.SimLJVacancy
-
- Ai - Variable in class etomica.potential.PotentialCalculationPhiSum
-
- ai - Variable in class etomica.rotation.DipoleBox
-
- ai - Variable in class etomica.rotation.DipoleBoxMatrix
-
- ai - Variable in class etomica.virial.simulations.SimulationVirial
-
- ai - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- ai - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- ai - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- aiInner - Variable in class etomica.atom.iterator.ApiInnerVariable
-
The iterators used to generate the sets of atoms.
- aiInner - Variable in class etomica.atom.iterator.ApiIntergroup
-
- aiInner - Variable in class etomica.molecule.iterator.MpiInnerVariable
-
The iterators used to generate the sets of atoms.
- aiInnerSize - Variable in class etomica.atom.iterator.ApiIntergroupExchange
-
- aiOuter - Variable in class etomica.atom.iterator.ApiInnerVariable
-
- aiOuter - Variable in class etomica.atom.iterator.ApiIntergroup
-
- aiOuter - Variable in class etomica.molecule.iterator.MpiInnerVariable
-
- aiOuter - Variable in class etomica.molecule.iterator.MpiIntraspecies1A
-
- aiOuterSize - Variable in class etomica.atom.iterator.ApiIntergroupExchange
-
- aj - Variable in class etomica.models.water.P2WaterSzalewicz
-
- Aj - Variable in class etomica.potential.PotentialCalculationPhiSum
-
- aj3 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- akima - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- akima - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- akima - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- akima - Variable in class etomica.overlap.DataOverlap
-
- akima - Variable in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
-
- AkimaSpline - Class in etomica.math.numerical
-
DataProcessor that interpolates incoming data using an Akima spline
interpolation scheme.
- AkimaSpline() - Constructor for class etomica.math.numerical.AkimaSpline
-
- akimaSpline - Variable in class etomica.models.nitrogen.FindTransitionTemperature
-
- akimaSpline - Variable in class etomica.normalmode.SoftSphereSolidEOS
-
- AkimaSplineSmoother - Class in etomica.math.numerical
-
Optimization algorithm which attempts to smooth data without moving any
point far from its original location.
- AkimaSplineSmoother(IRandom) - Constructor for class etomica.math.numerical.AkimaSplineSmoother
-
- AkimaSplineSmootherApp - Class in etomica.math.numerical
-
App to drive AkimaSplineSmoother
- AkimaSplineSmootherApp(String) - Constructor for class etomica.math.numerical.AkimaSplineSmootherApp
-
- AkimaSplineSmootherApp.Applet - Class in etomica.math.numerical
-
- AkimaSplineSmootherApp.IntegratorSmoother - Class in etomica.math.numerical
-
- AkimaSplineSmootherApp.PlotAction - Class in etomica.math.numerical
-
- AkimaSplineSmootherDy - Class in etomica.math.numerical
-
Optimization algorithm which attempts to smooth data without moving any
point far from its original location.
- AkimaSplineSmootherDy(IRandom) - Constructor for class etomica.math.numerical.AkimaSplineSmootherDy
-
- AkimaSplineSmootherDyApp - Class in etomica.math.numerical
-
App to drive AkimaSplineSmoother
- AkimaSplineSmootherDyApp(String) - Constructor for class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- AkimaSplineSmootherDyApp.Applet - Class in etomica.math.numerical
-
- AkimaSplineSmootherDyApp.IntegratorSmoother - Class in etomica.math.numerical
-
- AkimaSplineSmootherDyApp.PlotAction - Class in etomica.math.numerical
-
- AkimaSplineSmootherMain - Class in etomica.math.numerical
-
Main method to drive AkimaSplineSmoother
- AkimaSplineSmootherMain() - Constructor for class etomica.math.numerical.AkimaSplineSmootherMain
-
- AL10 - Static variable in class etomica.math.Gamma
-
- al1l2l0(int, int, int, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
-
- al1l2l0(int, int, int, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- Alat - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
-
- alfst - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- align - Variable in class etomica.graphics.DisplayBox
-
- align - Variable in class etomica.graphics.DisplayPolytope
-
- align_on_z_axis(Vector[], Vector[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- alignedV1 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- alignedV2 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- alkaneSpherePanel - Variable in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- all - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- all - Static variable in class org.jmol.script.Token
-
- allAtoms - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
-
- allAtoms - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- allAtoms - Variable in class etomica.data.meter.MeterRDFPC
-
- allatoms - Variable in class etomica.dimer.IntegratorDimerMin
-
- allatoms - Variable in class etomica.dimer.IntegratorDimerRT
-
- allAtoms - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
-
- allAtoms - Variable in class etomica.integrator.IntegratorVelocityVerlet
-
- allAtoms - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- allAtoms - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- allAtoms - Variable in class etomica.mappedvirial.MeterMappedU
-
- allAtoms - Variable in class etomica.mappedvirial.MeterMappedVirial
-
- allAtoms - Variable in class etomica.mappedvirial.MeterMappedVirialV
-
- allAtoms - Variable in class etomica.mappedvirial.MeterMeanForce
-
- allAtoms - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- allAtoms - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- allAtoms - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- allAtoms - Variable in class etomica.math.numerical.CalcGradientDifferentiable
-
- allAtoms - Variable in class etomica.modules.droplet.IntegratorDroplet
-
- allAtoms - Variable in class etomica.surfacetension.SurfaceTensionMapped
-
- allAtoms(IAtomList) - Static method in class etomica.util.Debug
-
determines if all of the atoms in the given array are set to be debugged
(via ATOMx_NUM and setAtoms(box)).
- allAtoms(IMoleculeList) - Static method in class etomica.util.Debug
-
determines if all of the atoms in the given array are set to be debugged
(via ATOMx_NUM and setAtoms(box)).
- allCoords - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- allCriteria - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- allCriteria - Variable in class etomica.nbr.list.PotentialMasterList
-
- AllData(long, IData, IData) - Constructor for class etomica.data.AccumulatorAverageBlockless.AllData
-
- allData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- allData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- allDone() - Method in class etomica.modules.clustergenerator.MyApplet.Starter
-
- allEdges - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- allfloat - Static variable in class org.jmol.script.Token
-
- AllIsomorphs - Class in etomica.graph.operations
-
Returns all graphs that are isomorphs of the original graph(s).
- AllIsomorphs() - Constructor for class etomica.graph.operations.AllIsomorphs
-
- AllIsomorphs.AllIsomorphsParameters - Class in etomica.graph.operations
-
- AllIsomorphsParameters(boolean) - Constructor for class etomica.graph.operations.AllIsomorphs.AllIsomorphsParameters
-
- AllIsomorphsParameters(boolean, Property) - Constructor for class etomica.graph.operations.AllIsomorphs.AllIsomorphsParameters
-
- allLnAlpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- allLnAlpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- allMoleculeList - Variable in class etomica.box.Box
-
- allMyData - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- allMyData - Variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- allMyData - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- allMyData - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- allMyData - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- allocateBitmap() - Method in class etomica.graph.model.impl.AbstractBitmap
-
Allocates the storage space for bitSize() bits.
- allocateBitmap() - Method in class etomica.graph.model.impl.BitmapOfLong
-
- allocateBitmap() - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- allocateColix(int) - Static method in class org.jmol.util.Colix
-
- allocateRgbImage(int, int, int[], int, boolean) - Method in interface org.jmol.api.ApiPlatform
-
- allocateRgbImage(int, int, int[], int, boolean) - Method in class org.jmol.awt.Platform
-
- allOr - Variable in class etomica.models.water.P2WaterSzalewicz
-
- allOr0 - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- allOr0 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- allOr0 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- allOr1 - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- allOr1 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- allOr1 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- ALLOWED - Static variable in enum etomica.units.Prefix
-
Constant used when invoking constructor of SimpleUnit class to indicate
that the unit permits the use of a prefix.
- allowedQuaternionFrames - Static variable in class org.jmol.viewer.JmolConstants
-
- allowedScriptTypes - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Set of allowed script types.
- allowembeddedscripts - Static variable in class org.jmol.script.Token
-
- allowgestures - Static variable in class org.jmol.script.Token
-
- allowkeystrokes - Static variable in class org.jmol.script.Token
-
- allowmodelkit - Static variable in class org.jmol.script.Token
-
- allowmoveatoms - Static variable in class org.jmol.script.Token
-
- allowmultitouch - Static variable in class org.jmol.script.Token
-
- allowrotateselected - Static variable in class org.jmol.script.Token
-
- allPermutations - Variable in class etomica.graph.operations.BiComponentSubst.BiComponentSubstParameters
-
- allPermutations - Variable in class etomica.graph.operations.FactorOnce.FactorOnceParameters
-
- allPermutations - Variable in class etomica.modules.clustergenerator.MyApplet
-
- allPermutations - Variable in class etomica.virial.cluster.VirialDiagrams
-
- allPermutations - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- allPermutations - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- allPermutations - Variable in class etomica.virial.ClusterICPYC
-
- allPermutationsCB - Variable in class etomica.modules.clustergenerator.MyApplet
-
- allPotentials - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- allPotentials - Variable in class etomica.nbr.PotentialMasterNbr
-
- allPotentials - Variable in class etomica.potential.PotentialMasterMonatomic
-
- AllSigs(int) - Constructor for class etomica.virial.ClusterWheatleyHS.AllSigs
-
- allVal - Variable in class etomica.virial.MayerHSMixture
-
- allValue - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- allValue - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- allValue - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- allValue - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- allValueClusters - Variable in class etomica.virial.simulations.SimulationVirial
-
- allWrappers() - Method in class etomica.meta.SimulationModel
-
- allZero - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- alpha - Variable in class etomica.dimer.P1LepsHarmonic
-
- alpha - Variable in class etomica.freeenergy.npath.SimLattice.LjMC3DParams
-
- alpha - Variable in class etomica.models.co2.P2CO2Hellmann
-
- alpha - Variable in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
-
- alpha - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- alpha - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- alpha - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- alpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
-
- alpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- alpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- alpha - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- alpha - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- alpha - Variable in class etomica.modules.adsorption.EOSSWPatel
-
- alpha - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- alpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- alpha - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- alpha - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- alpha - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
-
- alpha - Variable in class etomica.normalmode.MCMoveHarmonicEin
-
- alpha - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- alpha - Variable in class etomica.normalmode.MeterTargetTP
-
- alpha - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
-
- alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- alpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- alpha - Variable in class etomica.overlap.MeterOverlap
-
- alpha - Variable in class etomica.potential.EwaldSummation
-
- alpha - Variable in class etomica.potential.EwaldSumMolecules
-
- alpha - Static variable in class etomica.potential.P1HydrogenMielke
-
- alpha - Static variable in class etomica.potential.P2HePCKLJS
-
- alpha - Variable in class etomica.potential.P2NitrogenHellmann
-
- alpha - Variable in class etomica.potential.P3AxilrodTeller.MyAgent
-
- alpha - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- alpha - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- alpha - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- alpha - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- alpha - Variable in class etomica.potential.P3Induction
-
- alpha - Variable in class etomica.potential.P3Induction.MyAgent
-
- alpha1 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- alpha1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- alpha1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- alpha1 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- alpha2 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- alpha2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- alpha2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- alpha2 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- alpha2 - Variable in class etomica.potential.EwaldSummation
-
- alpha3 - Variable in class etomica.potential.EwaldSummation
-
- ALPHA_SHIFT - Static variable in class org.jmol.util.Colix
-
- alphaA - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- alphaA - Static variable in class etomica.potential.P2NitrogenHellmann
-
- alphaB - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- alphaB - Static variable in class etomica.potential.P2NitrogenHellmann
-
- alphaCenter - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- alphaCenter - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- alphaCenter - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- alphaCenter - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- alphaCenter - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- alphaCenter - Variable in class etomica.normalmode.MeterTargetTP
-
- alphaCenter - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- alphaCenter - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- alphaCenter - Variable in class etomica.overlap.MeterOverlap
-
- alphaCenter - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- alphaCenter - Variable in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- alphaChoice - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- alphaCoeffs - Variable in class etomica.models.nitrogen.FindTransitionTemperature
-
- alphaData - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- alphaData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- alphaData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- alphaData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- alphaData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- alphaFac - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- alphaInfo - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- alphaInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- alphaInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- alphaInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- alphaInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- alphaIso - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- alphaIsoSim - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- alphaPar - Variable in class etomica.models.co2.PNCO2GCPM
-
- alphaPar - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
-
- alphaPerp - Variable in class etomica.models.co2.PNCO2GCPM
-
- alphaPerp - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
-
- alphaPol - Variable in class etomica.models.water.PNWaterGCPM
-
- alphaSource - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- alphaSource - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- alphaSource - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- AlphaSource - Interface in etomica.overlap
-
Class that can return values of alpha.
- alphaSource - Variable in class etomica.overlap.DataOverlap
-
- alphaSource - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- alphaSpan - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- alphaSpan - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
-
- alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- alphaSpan - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- alphaSpan - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- alphaSpan - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- alphaSpan - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- alphaSpan - Variable in class etomica.normalmode.MeterTargetTP
-
- alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
-
- alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- alphaSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- alphaSpan - Variable in class etomica.overlap.MeterOverlap
-
- alphaSpan - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- alphaSpan - Variable in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- alphaTag - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- alphaTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- alphaTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- alphaTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- alphaTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- ALPREC - Static variable in class etomica.math.Gamma
-
- altArgbsCpk - Static variable in class org.jmol.viewer.JmolConstants
-
- altElementIndexFromNumber(int) - Static method in class org.jmol.util.Elements
-
- altElementMax - Static variable in class org.jmol.util.Elements
-
length of the altElementSymbols, altElementNames, altElementNumbers arrays
- altElementNameFromIndex(int) - Static method in class org.jmol.util.Elements
-
- altElementNumberFromIndex(int) - Static method in class org.jmol.util.Elements
-
- altElementSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
-
- alternateStylesheet - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Alternate stylesheet for which should be applied to the SVG
- altIsotopeSymbolFromIndex(int) - Static method in class org.jmol.util.Elements
-
- altIsotopeSymbolFromIndex2(int) - Static method in class org.jmol.util.Elements
-
- altloc - Static variable in class org.jmol.script.Token
-
- altVertices - Variable in class org.jmol.util.MeshSurface
-
- ambientFraction - Static variable in class org.jmol.util.Shader
-
- ambientpercent - Static variable in class org.jmol.script.Token
-
- ambientPercent - Static variable in class org.jmol.util.Shader
-
- Ampere - Class in etomica.units
-
The ampere unit of electrical current.
- AnalyticalDerivativeEnergyParacetamol - Class in etomica.paracetamol
-
- AnalyticalDerivativeEnergyParacetamol(Box, PotentialMaster, Space) - Constructor for class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- and(Bitmap) - Method in interface etomica.graph.model.Bitmap
-
and: bitmap -> bitmap = (bitmap & other).
- and(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- and(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong
-
TIME = O(1) for a compatible instance of other.
- and(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- and(BitSet) - Method in class org.jmol.util.BitSet
-
Performs a logical AND of this target bit set with the argument bit
set.
- andNot(BitSet) - Method in class org.jmol.util.BitSet
-
Clears all of the bits in this BitSet whose corresponding bit is
set in the specified BitSet.
- andNot(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
-
- angle - Variable in class etomica.lattice.crystal.Primitive
-
- angle - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- angle - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
-
- angle - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
-
- angle - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- angle - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- angle - Variable in class etomica.potential.P3BondAngle
-
- angle - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- angle - Variable in class etomica.space2d.Orientation2D
-
- Angle - Class in etomica.units.dimensions
-
Base for all angular units.
- angle() - Method in class etomica.units.systems.CGS
-
- angle() - Method in class etomica.units.systems.LJ
-
- angle() - Method in class etomica.units.systems.MKS
-
- angle() - Method in class etomica.units.systems.UnitSystem
-
- angle() - Method in class etomica.units.systems.UnitSystem.Sim
-
- angle - Static variable in class org.jmol.script.Token
-
- angle - Variable in class org.jmol.util.AxisAngle4f
-
The angle.
- angle(Vector3f) - Method in class org.jmol.util.Vector3f
-
Returns the angle in radians between this vector and the vector parameter;
the return value is constrained to the range [0,PI].
- angleCCC - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- angleCCC_half - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- angleCCH - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- angleHCH - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- angleHCH_half - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- angleHOH - Static variable in class etomica.models.water.ConformationWater3P
-
- angleHOH - Static variable in class etomica.models.water.ConformationWaterTIP4P
-
- anglePanel - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- angles - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- Angstrom - Class in etomica.units
-
- ANGSTROMS_PER_BOHR - Static variable in class org.jmol.viewer.JmolConstants
-
- angularMomentum - Variable in class etomica.molecule.MoleculeOrientedDynamic
-
- angularVelocity - Variable in class etomica.atom.AtomOrientedDynamic
-
- angularVelocity - Variable in class etomica.data.meter.MeterKineticEnergyRigid
-
- angularVelocity - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- animationfps - Static variable in class org.jmol.script.Token
-
- ANIntergroupCoupled - Class in etomica.atom.iterator
-
Iterator that returns coupled iterates of any size; the first set contains
the first atom from each basis.
- ANIntergroupCoupled(int) - Constructor for class etomica.atom.iterator.ANIntergroupCoupled
-
- ANIntergroupExchange - Class in etomica.atom.iterator
-
- ANIntergroupExchange(int) - Constructor for class etomica.atom.iterator.ANIntergroupExchange
-
- anIntragroupExchange - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- ANIntragroupExchange - Class in etomica.atom.iterator
-
- ANIntragroupExchange(int, int) - Constructor for class etomica.atom.iterator.ANIntragroupExchange
-
- anoise - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- antialiasdisplay - Static variable in class org.jmol.script.Token
-
- antialiasEnabled - Variable in class org.jmol.util.GData
-
- antialiasimages - Static variable in class org.jmol.script.Token
-
- antialiasThisFrame - Variable in class org.jmol.util.GData
-
- antialiastranslucent - Static variable in class org.jmol.script.Token
-
- aNumber - Variable in class etomica.modules.materialfracture.MeterElongation
-
- aNumber - Variable in class etomica.modules.materialfracture.MeterStrain
-
- anx - Static variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- anyAtom(IAtomList) - Static method in class etomica.util.Debug
-
determines whether any of the atoms in the given array are set to be debugged
(via ATOMx_NUM)
- anyMolecule(IMoleculeList) - Static method in class etomica.util.Debug
-
determines whether any of the atoms in the given array are set to be debugged
(via ATOMx_NUM)
- apacheErfc() - Method in class etomica.math.ErfcBenchmark
-
- apacheFactorial() - Method in class etomica.math.FactorialBenchmark
-
- apacheLnFactorial() - Method in class etomica.math.LnFactorialBenchmark
-
- aPair - Variable in class etomica.virial.MayerGeneralAtomic
-
- aPairSet - Variable in class etomica.virial.BoxCluster
-
- api - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- Api1ACell - Class in etomica.nbr.cell
-
Generates pairs that are cell-based neighbors of a specific Atom.
- Api1ACell(int, double, BoxAgentManager) - Constructor for class etomica.nbr.cell.Api1ACell
-
Constructor makes iterator that must have box specified and then be
reset() before iteration.
- Api1ASite - Class in etomica.nbr.site
-
Iteration is performed using site lists.
- Api1ASite(int, BoxAgentManager) - Constructor for class etomica.nbr.site.Api1ASite
-
Constructor makes iterator that must have box specified and then be
reset() before iteration.
- ApiAACell - Class in etomica.nbr.cell
-
Returns iterates formed from all cell-based neighbor pairs.
- ApiAACell(int, double, Box) - Constructor for class etomica.nbr.cell.ApiAACell
-
Constructor makes iterator that must have box specified and then be
reset() before iteration.
- ApiBuilder - Class in etomica.atom.iterator
-
Provides static methods for construction of some useful pair iterators.
- apiDown - Variable in class etomica.molecule.iterator.MpiIntraspecies1A
-
- ApiFilteredCylinder - Class in etomica.modules.pistoncylinder
-
Our own ApiFiltered that's box-dependent
- ApiFilteredCylinder(ApiFilteredCylinder.AtomFilterInCylinder) - Constructor for class etomica.modules.pistoncylinder.ApiFilteredCylinder
-
- ApiFilteredCylinder.AtomFilterInCylinder - Class in etomica.modules.pistoncylinder
-
Filter to expclude any pair with an atom within some distance from a
wall.
- ApiIndexList - Class in etomica.atom.iterator
-
Iterator that returns intramolecular pairs of atoms with specific indices.
- ApiIndexList(int[][]) - Constructor for class etomica.atom.iterator.ApiIndexList
-
Constructs iterator without defining atoms in pair.
- ApiInnerVariable - Class in etomica.atom.iterator
-
Pair iterator synthesized from two atom iterators, such that the inner-loop
iteration depends on the outer-loop atom.
- ApiInnerVariable(AtomIterator, AtomIteratorAtomDependent) - Constructor for class etomica.atom.iterator.ApiInnerVariable
-
Construct a pair iterator using the given atom iterators.
- ApiInnerVariable(AtomIterator, AtomIteratorAtomDependent, boolean) - Constructor for class etomica.atom.iterator.ApiInnerVariable
-
Construct a pair iterator using the given atom iterators, indicating
whether the atoms ordering in the AtomPair should be swapped from the
default behavior.
- ApiInterArrayList - Class in etomica.atom.iterator
-
Returns all pairs formed from two different untabbed lists of atoms.
- ApiInterArrayList() - Constructor for class etomica.atom.iterator.ApiInterArrayList
-
Construct iterator with an empty lists.
- ApiInterArrayList(IAtomList, IAtomList) - Constructor for class etomica.atom.iterator.ApiInterArrayList
-
Constructs iterator to return pairs from the given lists.
- ApiIntergroup - Class in etomica.atom.iterator
-
Iterator that returns pairs formed using two different basis atoms, so that
the iterates are taken from two different groups.
- ApiIntergroup() - Constructor for class etomica.atom.iterator.ApiIntergroup
-
Default iterator is an ApiInnerFixed formed from two AtomIteratorBasis
instances.
- ApiIntergroup(AtomIteratorBasisDependent, AtomIteratorBasisDependent) - Constructor for class etomica.atom.iterator.ApiIntergroup
-
Constructs a pair iterator that returns iterates from the given
pairIterator, which is expected to contain two basis-dependent
iterators.
- ApiIntergroupCoupled - Class in etomica.atom.iterator
-
Iterator that returns coupled iterates; the first pair contains the first
atom from each basis.
- ApiIntergroupCoupled() - Constructor for class etomica.atom.iterator.ApiIntergroupCoupled
-
- ApiIntergroupCoupled(AtomIteratorBasis, AtomIteratorBasis) - Constructor for class etomica.atom.iterator.ApiIntergroupCoupled
-
- ApiIntergroupExchange - Class in etomica.atom.iterator
-
- ApiIntergroupExchange(int) - Constructor for class etomica.atom.iterator.ApiIntergroupExchange
-
- ApiIntergroupIntraSpecies - Class in etomica.atom.iterator
-
Iterator that returns pairs formed using two different basis atoms, so that
the iterates are taken from two different groups.
- ApiIntergroupIntraSpecies(AtomIteratorBasisDependent, AtomIteratorBasisDependent) - Constructor for class etomica.atom.iterator.ApiIntergroupIntraSpecies
-
Constructs a pair iterator that returns iterates from the given
pairIterator, which is expected to contain two basis-dependent
iterators.
- ApiIntraArrayList - Class in etomica.atom.iterator
-
Returns all pairs formed from a single list of atoms.
- ApiIntraArrayList() - Constructor for class etomica.atom.iterator.ApiIntraArrayList
-
Construct iterator with an empty list.
- ApiIntraArrayList(IAtomList) - Constructor for class etomica.atom.iterator.ApiIntraArrayList
-
Constructs iterator to return pairs from the given list.
- ApiIntragroup - Class in etomica.atom.iterator
-
Returns iterates from the childList of a single basis atom.
- ApiIntragroup() - Constructor for class etomica.atom.iterator.ApiIntragroup
-
Constructor makes iterator that must have basis specified and then be
reset() before iteration.
- ApiIntragroup(AtomIteratorAtomDependent, AtomIteratorAtomDependent) - Constructor for class etomica.atom.iterator.ApiIntragroup
-
- ApiIntragroup(AtomsetIteratorBasisDependent, AtomIteratorAtomDependent, AtomIteratorAtomDependent) - Constructor for class etomica.atom.iterator.ApiIntragroup
-
- ApiLeafAtoms - Class in etomica.atom.iterator
-
Iterator that returns all pairs that can be formed from all leaf atoms of a
given box.
- ApiLeafAtoms() - Constructor for class etomica.atom.iterator.ApiLeafAtoms
-
Creates new pair iterator that requires reset() before beginning
iteration.
- ApiPlatform - Interface in org.jmol.api
-
- apiPlatform - Variable in class org.jmol.util.GData
-
- APIPotentialReference(MeterHarmonicEnergy[]) - Constructor for class etomica.normalmode.SimOverlapLJModule.APIPotentialReference
-
- APIPotentialTarget(PotentialMaster) - Constructor for class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
-
- apiUp - Variable in class etomica.molecule.iterator.MpiIntraspecies1A
-
- APP_NAME - Static variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- AppControllerMixtureBuilder - Class in etomica.virial.GUI.controllers
-
- AppControllerMixtureBuilder(AppViewMixtureBuilder, AppModelMixtureBuilder) - Constructor for class etomica.virial.GUI.controllers.AppControllerMixtureBuilder
-
- append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialAlkaneEHTest
-
- append(double[], double[]) - Static method in class etomica.virial.simulations.VirialAlkaneEHTest
-
- append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialAlkaneFlex
-
- append(double[], double[]) - Static method in class etomica.virial.simulations.VirialAlkaneFlex
-
- append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialCO2PI
-
- append(double[], double[]) - Static method in class etomica.virial.simulations.VirialCO2PI
-
- append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialH2PI
-
- append(double[], double[]) - Static method in class etomica.virial.simulations.VirialH2PI
-
- append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialH2PIBoltzmann
-
- append(double[], double[]) - Static method in class etomica.virial.simulations.VirialH2PIBoltzmann
-
- append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialH2PIXC
-
- append(double[], double[]) - Static method in class etomica.virial.simulations.VirialH2PIXC
-
- append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePI
-
- append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePI
-
- append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePI_PotentialCorrection
-
- append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePI_PotentialCorrection
-
- append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePIXC
-
- append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePIXC
-
- append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePIXCEven
-
- append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePIXCEven
-
- append(ClusterBonds[], ClusterBonds[]) - Static method in class etomica.virial.simulations.VirialHePIXCOdd
-
- append(double[], double[]) - Static method in class etomica.virial.simulations.VirialHePIXCOdd
-
- append(String) - Method in class org.jmol.util.StringXBuilder
-
- appendB(boolean) - Method in class org.jmol.util.StringXBuilder
-
- appendC(char) - Method in class org.jmol.util.StringXBuilder
-
- appendCB(char[], int, int) - Method in class org.jmol.util.StringXBuilder
-
- appendD(double) - Method in class org.jmol.util.StringXBuilder
-
- appendF(float) - Method in class org.jmol.util.StringXBuilder
-
note that JavaScript could drop off the ".0" in "1.0"
- appendI(int) - Method in class org.jmol.util.StringXBuilder
-
- appendnew - Static variable in class org.jmol.script.Token
-
- appendO(Object) - Method in class org.jmol.util.StringXBuilder
-
- appendSB(StringXBuilder) - Method in class org.jmol.util.StringXBuilder
-
- AppFrameMixtureBuilder - Class in etomica.virial.GUI.containers
-
- AppFrameMixtureBuilder(String) - Constructor for class etomica.virial.GUI.containers.AppFrameMixtureBuilder
-
- Applet() - Constructor for class etomica.graphics.DisplayPolytope.Applet
-
- Applet() - Constructor for class etomica.math.numerical.AkimaSplineSmootherApp.Applet
-
- Applet() - Constructor for class etomica.math.numerical.AkimaSplineSmootherDyApp.Applet
-
- Applet() - Constructor for class etomica.modules.adsorption.AdsorptionGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.catalysis.CatalysisGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.chainequilibrium.ChainEquilibriumGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.colloid.ColloidGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.crystalviewer.CrystalViewer.Applet
-
- Applet() - Constructor for class etomica.modules.dcvgcmd.DCVGCMDGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.droplet.DropletAtomicGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.droplet.DropletGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.ensembles.LJMCGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.entropylottery.EntropyLotteryGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.insertion.InsertionGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.joulethomson.JouleThomson.Applet
-
- Applet() - Constructor for class etomica.modules.ljmd.LjmdGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.materialfracture.MaterialFractureGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.mu.MuGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.Applet
-
- Applet() - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphicMC.Applet
-
- Applet() - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.Applet
-
- Applet() - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.Applet
-
- Applet() - Constructor for class etomica.modules.osmosis.Osmosis.Applet
-
- Applet() - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.rheology.RheologyGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.sam.SamGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.swmd.SwmdGraphic.Applet
-
- Applet() - Constructor for class etomica.modules.vle.B2Fit.Applet
-
- Applet() - Constructor for class etomica.modules.vle.VLE.Applet
-
- Applet() - Constructor for class etomica.normalmode.HTTPSoftSphereApplet.Applet
-
- Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay1D.Applet
-
- Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic.Applet
-
- Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic.Applet
-
- Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay3D.Applet
-
- Applet() - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic.Applet
-
- Applet() - Constructor for class etomica.normalmode.nptdemo.HSNPT2DGraphic.Applet
-
- Applet() - Constructor for class etomica.normalmode.SimLJVacancy.Applet
-
- Applet() - Constructor for class etomica.rotation.DipoleBox.Applet
-
- Applet() - Constructor for class etomica.rotation.DipoleBoxMatrix.Applet
-
- Applet() - Constructor for class etomica.rotation.SingleDipole.Applet
-
- Applet() - Constructor for class etomica.rotation.SingleDumbellRattle.Applet
-
- Applet() - Constructor for class etomica.rotation.SingleDumbellShake.Applet
-
- Applet() - Constructor for class etomica.rotation.SingleWater.Applet
-
- Applet() - Constructor for class etomica.rotation.SingleWaterMatrix.Applet
-
- Applet() - Constructor for class etomica.rotation.SingleWaterRattle.Applet
-
- Applet() - Constructor for class etomica.rotation.SingleWaterShake.Applet
-
- Applet() - Constructor for class etomica.rotation.WaterBox.Applet
-
- Applet() - Constructor for class etomica.rotation.WaterDroplet.Applet
-
- Applet() - Constructor for class etomica.rotation.WaterDropletMatrix.Applet
-
- Applet() - Constructor for class etomica.rotation.WaterDropletRattle.Applet
-
- Applet() - Constructor for class etomica.rotation.WaterDropletShake.Applet
-
- Applet() - Constructor for class etomica.rotation.WaterTrimer.Applet
-
- Applet() - Constructor for class etomica.rotation.WaterTrimerRattle.Applet
-
- Applet() - Constructor for class etomica.rotation.WaterTrimerShake.Applet
-
- Applet() - Constructor for class etomica.simulation.prototypes.LJMD3D.Applet
-
- Applet() - Constructor for class etomica.thermointegration.LjMc3D.Applet
-
- appletproxy - Static variable in class org.jmol.script.Token
-
- ApplicationMixtureBuilder - Class in etomica.virial.GUI
-
- ApplicationMixtureBuilder() - Constructor for class etomica.virial.GUI.ApplicationMixtureBuilder
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.AllIsomorphs
-
- apply(Graph, AllIsomorphs.AllIsomorphsParameters) - Method in class etomica.graph.operations.AllIsomorphs
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.BiComponentSubst
-
- apply(Graph, BiComponentSubst.BiComponentSubstParameters) - Method in class etomica.graph.operations.BiComponentSubst
-
- apply(Set<Graph>, Set<Graph>, Parameters) - Method in interface etomica.graph.operations.Binary
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.CombineABSite
-
- apply(Graph, CombineABSite.CombineABSiteParameters) - Method in class etomica.graph.operations.CombineABSite
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.ComponentSubst
-
- apply(Graph, ComponentSubst.ComponentSubstParameters) - Method in class etomica.graph.operations.ComponentSubst
-
- apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Conv
-
- apply(Graph, Graph, ConvParameters) - Method in class etomica.graph.operations.Conv
-
- apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Decorate
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DecorateWertheim2Site
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DecorateWertheim2SiteRho
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DecorateWertheim3SiteRho
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho
-
- apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Delete
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DeleteEdge
-
- apply(Graph, DeleteEdgeParameters) - Method in class etomica.graph.operations.DeleteEdge
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DifByConstant
-
- apply(Graph, DifByConstant.DifByConstantParameters) - Method in class etomica.graph.operations.DifByConstant
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DifByEdge
-
- apply(Graph, DifParameters) - Method in class etomica.graph.operations.DifByEdge
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.DifByNode
-
- apply(Graph) - Method in class etomica.graph.operations.DropOrphanNodes
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Exclude
-
- apply(Graph, ExcludeParameters) - Method in class etomica.graph.operations.Exclude
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Exp
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Factor
-
- apply(Graph, MulFlexible.MulFlexibleParameters) - Method in class etomica.graph.operations.Factor
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.FactorOnce
-
- apply(Graph, FactorOnce.FactorOnceParameters) - Method in class etomica.graph.operations.FactorOnce
-
- apply(Graph, List<Integer>, List<Integer>) - Method in class etomica.graph.operations.FactorOnce
-
- apply(Graph, List<Byte>) - Method in class etomica.graph.operations.GraphExtract
-
- apply(Graph) - Method in interface etomica.graph.operations.GraphOp
-
- apply(Graph) - Method in class etomica.graph.operations.GraphOp.GraphOpNull
-
- apply(Graph) - Method in class etomica.graph.operations.GraphOpMaxRoot
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.IdenticalFree
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Int
-
- apply(Graph, IntParameters) - Method in class etomica.graph.operations.Int
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.IsoFree
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.MaxIsomorph
-
- apply(Graph, MaxIsomorph.MaxIsomorphParameters) - Method in class etomica.graph.operations.MaxIsomorph
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.MaxIsomorphWertheim
-
- apply(Graph, MaxIsomorphWertheim.MaxIsomorphWertheimParameters) - Method in class etomica.graph.operations.MaxIsomorphWertheim
-
- apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Mul
-
- apply(Graph, Graph, Mul.MulParameters) - Method in class etomica.graph.operations.Mul
-
- apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.MulFlexible
-
- apply(Set<Graph>, Set<Graph>[], Parameters) - Method in class etomica.graph.operations.MulFlexible
-
- apply(Graph, Graph, MulFlexible.MulFlexibleParameters) - Method in class etomica.graph.operations.MulFlexible
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.MulScalar
-
- apply(Graph, MulScalarParameters) - Method in class etomica.graph.operations.MulScalar
-
- apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.MulUnion
-
- apply(Graph, Graph) - Method in class etomica.graph.operations.MulUnion
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.NCopy
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.PCopy
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Pow
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.ReeHoover
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Relabel
-
- apply(Graph, RelabelParameters) - Method in class etomica.graph.operations.Relabel
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.RelabelWertheim
-
- apply(Graph, RelabelParameters) - Method in class etomica.graph.operations.RelabelWertheim
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.SetPropertyFilter
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Split
-
- apply(Graph, SplitParameters) - Method in class etomica.graph.operations.Split
-
- apply(Graph) - Method in class etomica.graph.operations.SplitGraph
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.SplitOne
-
- apply(Graph, SplitOne.SplitOneParameters) - Method in class etomica.graph.operations.SplitOne
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.SplitOneBiconnected
-
- apply(Graph, SplitOneBiconnected.SplitOneParametersBC) - Method in class etomica.graph.operations.SplitOneBiconnected
-
- apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Sub
-
- apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Sum
-
- apply(Set<Graph>, Parameters) - Method in interface etomica.graph.operations.Unary
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.UnaryChain
-
- apply(Graph, MulScalarParameters) - Method in class etomica.graph.operations.UnaryChain
-
- apply(Set<Graph>, Parameters) - Method in class etomica.graph.operations.Unfactor
-
- apply(Graph, MulFlexible.MulFlexibleParameters) - Method in class etomica.graph.operations.Unfactor
-
- apply(Set<Graph>, Set<Graph>, Parameters) - Method in class etomica.graph.operations.Union
-
- apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.BondConnectedSubstitution
-
- apply(Graph, BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site) - Method in class etomica.virial.cluster.BondConnectedSubstitution
-
- apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.BondConnectedSubstitution3Site
-
- apply(Graph, BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site) - Method in class etomica.virial.cluster.BondConnectedSubstitution3Site
-
- apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene
-
- apply(Graph, BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa) - Method in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene
-
- apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.CondenseExchange
-
- apply(Graph, CondenseExchange.CondenseExchangeParameters) - Method in class etomica.virial.cluster.CondenseExchange
-
- apply(Set<Graph>, Parameters) - Method in class etomica.virial.cluster.ExchangeSplit
-
- applyAnaglygh(EnumStereoMode, int[]) - Method in class org.jmol.g3d.Graphics3D
-
- applyAnaglygh(EnumStereoMode, int[]) - Method in class org.jmol.util.GData
-
- applyBlueAnaglyph() - Method in class org.jmol.g3d.Graphics3D
-
- applyColorTranslucencyLevel(short, float) - Static method in class org.jmol.util.Colix
-
- applyCustomAnaglyph(int[]) - Method in class org.jmol.g3d.Graphics3D
-
- applyCyanAnaglyph() - Method in class org.jmol.g3d.Graphics3D
-
- applyExponentPattern(String) - Method in class etomica.util.ScientificFormat
-
- applyGreenAnaglyph() - Method in class org.jmol.g3d.Graphics3D
-
- applyLocalizedPattern(String) - Method in class etomica.util.ScientificFormat
-
- applyMantissaPattern(String) - Method in class etomica.util.ScientificFormat
-
- applyPattern(String) - Method in class etomica.util.ScientificFormat
-
apply this pattern
- applysymmetrytobonds - Static variable in class org.jmol.script.Token
-
- applyTranslationRotation() - Method in class etomica.math.geometry.Polytope
-
Calculate transformed vertices from current values of vertices, position,
and orientation.
- AppModelMixtureBuilder - Class in etomica.virial.GUI.models
-
- AppModelMixtureBuilder() - Constructor for class etomica.virial.GUI.models.AppModelMixtureBuilder
-
- appName - Variable in class etomica.graphics.SimulationGraphic
-
- approx(float, float) - Static method in class org.jmol.util.Parser
-
- AppViewMixtureBuilder - Class in etomica.virial.GUI.views
-
- AppViewMixtureBuilder(AppFrameMixtureBuilder, AppModelMixtureBuilder) - Constructor for class etomica.virial.GUI.views.AppViewMixtureBuilder
-
- aProj - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- area - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Output AOI area.
- Area - Class in etomica.units.dimensions
-
Base for all area units.
- area() - Method in class etomica.units.systems.CGS
-
- area() - Method in class etomica.units.systems.LJ
-
- area() - Method in class etomica.units.systems.MKS
-
- area() - Method in class etomica.units.systems.UnitSystem
-
- area() - Method in class etomica.units.systems.UnitSystem.Sim
-
- areBonded(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
This function tells you if two atoms are bonded
This could probably be public, although a public version would
need to first re-retrieve agents
- areBonded(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
This function tells you if two atoms are bonded
- areEqual(ScriptVariable, ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- areEqual(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
-
- aRef - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
-
- aRef - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
-
- aRef - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
-
- aRef - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- arep - Variable in class etomica.potential.P2HydrogenHinde
-
- arep - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- aResidualFcc(double, double) - Static method in class etomica.statmech.LennardJones
-
Molar Helmholtz free energy for the fcc solid, in excess of an ideal gas at the
same temperature and density.
- arg() - Method in class etomica.math.Complex
-
Argument of this Complex number, the angle in radians with the x-axis in polar coordinates.
- argbCurrent - Variable in class org.jmol.util.GData
-
- argbsAmino - Static variable in class org.jmol.viewer.JmolConstants
-
- argbsChainAtom - Static variable in class org.jmol.viewer.JmolConstants
-
some pastel colors
C0D0FF - pastel blue
B0FFB0 - pastel green
B0FFFF - pastel cyan
FFC0C8 - pink
FFC0FF - pastel magenta
FFFF80 - pastel yellow
FFDEAD - navajowhite
FFD070 - pastel gold
FF9898 - light coral
B4E444 - light yellow-green
C0C000 - light olive
FF8060 - light tomato
00FF7F - springgreen
cpk on; select atomno>100; label %i; color chain; select selected & hetero; cpk off
- argbsChainHetero - Static variable in class org.jmol.viewer.JmolConstants
-
- argbsCpk - Static variable in enum org.jmol.constant.EnumPalette
-
Default table of CPK atom colors.
- argbsCpkRasmol - Static variable in enum org.jmol.constant.EnumPalette
-
- argbsFormalCharge - Static variable in class org.jmol.viewer.JmolConstants
-
- argbShapelyBackbone - Static variable in class org.jmol.viewer.JmolConstants
-
- argbShapelyDefault - Static variable in class org.jmol.viewer.JmolConstants
-
- argbShapelySpecial - Static variable in class org.jmol.viewer.JmolConstants
-
- argbsIsosurfaceNegative - Static variable in class org.jmol.viewer.JmolConstants
-
- argbsIsosurfacePositive - Static variable in class org.jmol.viewer.JmolConstants
-
- argbsRoygbScale - Static variable in class org.jmol.viewer.JmolConstants
-
- argbsRwbScale - Static variable in class org.jmol.viewer.JmolConstants
-
- argbsShapely - Static variable in class org.jmol.viewer.JmolConstants
-
- Argon - Class in etomica.chem.elements
-
Class for the Argon element.
- Argon(String) - Constructor for class etomica.chem.elements.Argon
-
- Argon(String, double) - Constructor for class etomica.chem.elements.Argon
-
- args - Variable in class etomica.graph.view.rasterizer.Main
-
List of arguments describing the conversion task to be
performed.
- array - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- array - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- array - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- array - Static variable in class org.jmol.script.Token
-
- ArrayA2B - Class in etomica.normalmode
-
Reads a file containing n mxm matrices as ASCII and serializes them to
another file.
- ArrayA2B() - Constructor for class etomica.normalmode.ArrayA2B
-
- ArrayB2A - Class in etomica.normalmode
-
Reads a file containing n mxm matrices as (serialized) binary data and
writes them to another file as text (ASCII).
- ArrayB2A() - Constructor for class etomica.normalmode.ArrayB2A
-
- arrayCollect(String[], String[]) - Static method in class etomica.util.Strings
-
Takes the elements of two string arrays and collects them
into a new array containing both sets of strings.
- arrayCopyBool(boolean[], int) - Static method in class org.jmol.util.ArrayUtil
-
- arrayCopyByte(byte[], int) - Static method in class org.jmol.util.ArrayUtil
-
- arrayCopyF(float[], int) - Static method in class org.jmol.util.ArrayUtil
-
- arrayCopyI(int[], int) - Static method in class org.jmol.util.ArrayUtil
-
- arrayCopyII(int[][], int) - Static method in class org.jmol.util.ArrayUtil
-
- arrayCopyObject(Object, int) - Static method in class org.jmol.util.ArrayUtil
-
note -- cannot copy if array is null!
- arrayCopyPt(Point3f[], int) - Static method in class org.jmol.util.ArrayUtil
-
- arrayCopyRangeI(int[], int, int) - Static method in class org.jmol.util.ArrayUtil
-
a specialized method that allows copying from a starting point either
to the end or to the middle (color schemes, especially)
- arrayCopyRangeRevI(int[], int, int) - Static method in class org.jmol.util.ArrayUtil
-
- arrayCopyS(String[], int) - Static method in class org.jmol.util.ArrayUtil
-
- arrayCopyShort(short[], int) - Static method in class org.jmol.util.ArrayUtil
-
- arrayIndex(int[]) - Method in class etomica.lattice.RectangularLattice
-
Returns the index in the 1-d array for the site corresponding
to the given lattice index.
- ArrayMoleculeDisplayList - Class in etomica.virial.GUI.components
-
- ArrayMoleculeDisplayList() - Constructor for class etomica.virial.GUI.components.ArrayMoleculeDisplayList
-
- ArrayProperty - Class in etomica.meta.properties
-
Container class for mapping an instance to an array property.
- ArrayProperty(Object, PropertyDescriptor) - Constructor for class etomica.meta.properties.ArrayProperty
-
- ArrayReader1D - Class in etomica.math.numerical
-
Reads in lots of 1D arrays from a file.
- ArrayReader1D() - Constructor for class etomica.math.numerical.ArrayReader1D
-
- ArrayReader1D - Class in etomica.normalmode
-
Reads in lots of 1D arrays from a file.
- ArrayReader1D() - Constructor for class etomica.normalmode.ArrayReader1D
-
- ArrayReader2D - Class in etomica.normalmode
-
Reads in lots of 2D arrays from a file.
- ArrayReader2D() - Constructor for class etomica.normalmode.ArrayReader2D
-
- Arrays - Class in etomica.util
-
Non-instantiable class with static utility methods for working with arrays.
- arrayShape - Variable in class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
-
- arrayShape - Variable in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
-
- ArrayUtil - Class in org.jmol.util
-
- ArrayUtil() - Constructor for class org.jmol.util.ArrayUtil
-
- ArticulatedAt0(boolean) - Constructor for class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
-
- ArticulatedAt0(boolean, char) - Constructor for class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
-
- ArticulatedAt0(boolean) - Constructor for class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
-
- ArticulatedAt0(boolean, char) - Constructor for class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
-
- articulationPair - Variable in class etomica.graph.property.FFTDecomposition
-
- articulationPoints - Variable in class etomica.graph.property.HasSimpleArticulationPoint
-
- asBoolean() - Method in class org.jmol.script.ScriptVariable
-
- asFloat() - Method in class org.jmol.script.ScriptVariable
-
- asin(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The inverse trigonometric sine.
- asinh(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The inverse hyperbolic sine.
- asInt() - Method in class org.jmol.script.ScriptVariable
-
- Asolid(double) - Static method in class etomica.statmech.HardSphereFluid
-
Returns the difference between absolute free energies between the given
densities for solid (FCC) hard spheres.
- Asolid(double, int) - Static method in class etomica.statmech.HardSphereFluid
-
Returns the difference between absolute free energies between the given
densities for solid (FCC) hard spheres.
- Asolid(double) - Static method in class etomica.statmech.HardSphereSolid
-
Returns the difference between absolute free energies between the given
densities for solid (FCC) hard spheres.
- Asolid(double, int) - Static method in class etomica.statmech.HardSphereSolid
-
- aspectRatio - Variable in class etomica.surfacetension.LJMC.LJMCParams
-
- assignCell(IMolecule) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Assigns the cell for the given atom.
- assignCell(IAtom) - Method in class etomica.nbr.cell.NeighborCellManager
-
Assigns the cell for the given atom.
- assignCellAll() - Method in interface etomica.box.BoxCellManager
-
Assigns cells to all molecules in the box.
- assignCellAll() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Assigns cells to all interacting atoms in the box.
- assignCellAll() - Method in class etomica.nbr.cell.NeighborCellManager
-
Assigns cells to all interacting atoms in the box.
- assignCellAll() - Method in class etomica.nbr.site.NeighborSiteManager
-
Should not be called, because cell assignments are made as atoms are created.
- assignColumnFrom(int, double[]) - Method in class etomica.data.types.DataDoubleArray
-
Assigns values in given array to the i-th "hypercolumn" of this data array.
- assignColumnFrom(int, BigDecimal[]) - Method in class etomica.data.types.DataDoubleBDArray
-
Assigns values in given array to the i-th "hypercolumn" of this data array.
- assignColumnTo(int, double[]) - Method in class etomica.data.types.DataDoubleArray
-
Assigns values in the i=th "hypercolumn" of this array to the given array.
- assignColumnTo(int, BigDecimal[]) - Method in class etomica.data.types.DataDoubleBDArray
-
Assigns values in the i=th "hypercolumn" of this array to the given array.
- AssignmentImpl - Class in etomica.graph.engine.impl
-
- AssignmentImpl(Parser.Variable, Parser.StrictExpression) - Constructor for class etomica.graph.engine.impl.AssignmentImpl
-
- assignSubsectionFrom(int[], double[]) - Method in class etomica.data.types.DataDoubleArray
-
Assigns values in the given array to the subsection of this array
beginning at the specified index.
- assignSubsectionFrom(int[], double[]) - Method in class etomica.data.types.DataDoubleBDArray
-
Assigns values in the given array to the subsection of this array
beginning at the specified index.
- assignTo(double[]) - Method in interface etomica.data.IData
-
Fills the given array with the values held by this Data instance.
- assignTo(double[]) - Method in class etomica.data.types.DataDouble
-
Returns a new one-element array formed from the current value of this
instance.
- assignTo(double[]) - Method in class etomica.data.types.DataDoubleArray
-
Returns the encapsulated array, implementing the Data interface.
- assignTo(double[]) - Method in class etomica.data.types.DataDoubleBDArray
-
Returns the encapsulated array, implementing the Data interface.
- assignTo(double[]) - Method in class etomica.data.types.DataGroup
-
- assignTo(double[]) - Method in class etomica.data.types.DataTable
-
Returns a new array formed from the values held by the data instance.
- assignTo(double[]) - Method in class etomica.data.types.DataTensor
-
Returns a new array formed by the elements of the wrapped tensor.
- assignTo(double[]) - Method in class etomica.data.types.DataVector
-
Assigns the elements of the wrapped vector to the given array.
- assignTo(Vector[]) - Method in interface etomica.space.Tensor
-
Assigns the tensor elements column-wise to the given vectors.
- assignTo(double[]) - Method in interface etomica.space.Tensor
-
Fills the given array with the elements of this tensor.
- assignTo(double[][]) - Method in interface etomica.space.Tensor
-
Fills the given 2-dimensional array with the elements of this tensor.
- assignTo(double[]) - Method in interface etomica.space.Vector
-
Assigns the components of this vector to the elements of the given array.
- assignTo(Vector[]) - Method in class etomica.space1d.Tensor1D
-
- assignTo(double[]) - Method in class etomica.space1d.Tensor1D
-
- assignTo(double[][]) - Method in class etomica.space1d.Tensor1D
-
- assignTo(double[]) - Method in class etomica.space1d.Vector1D
-
- assignTo(Vector[]) - Method in class etomica.space2d.Tensor2D
-
- assignTo(double[]) - Method in class etomica.space2d.Tensor2D
-
- assignTo(double[][]) - Method in class etomica.space2d.Tensor2D
-
- assignTo(double[]) - Method in class etomica.space2d.Vector2D
-
- assignTo(Vector[]) - Method in class etomica.space3d.Tensor3D
-
- assignTo(double[]) - Method in class etomica.space3d.Tensor3D
-
- assignTo(double[][]) - Method in class etomica.space3d.Tensor3D
-
- assignTo(double[]) - Method in class etomica.space3d.Vector3D
-
- assignTo(Vector[]) - Method in class etomica.spaceNd.TensorND
-
- assignTo(double[]) - Method in class etomica.spaceNd.TensorND
-
- assignTo(double[][]) - Method in class etomica.spaceNd.TensorND
-
- assignTo(double[]) - Method in class etomica.spaceNd.VectorND
-
- assignToBasket(int, int[]) - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
-
Allows the user to choose which wavevectors are in which basket.
- association(MayerFunction, MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterAceticAcid
-
- association(MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- association(MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- association(MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- association2(MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- association2(MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- association2(MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- association3(MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- association3(MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- association3(MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- association4(MoleculePair, MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- association4(MoleculePair, MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- association4(MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- association5(MoleculePair, MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- association5(MoleculePair, MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- association6(MoleculePair, MoleculePair, Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- AssociationDefinition - Interface in etomica.association
-
Interface for a method that defines whether two atoms are considered associated.
- AssociationDefinitionMolecule - Interface in etomica.association
-
Interface for a method that defines whether two molecules are considered associated.
- associationEnergy - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
-
- associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
-
- associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
-
- associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
-
- associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
-
- associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
-
- associationEnergy - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
-
- associationHelper - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- associationHelper - Variable in class etomica.association.ColorSchemeSmer
-
- associationHelper - Variable in class etomica.association.ColorSchemeSmerByLength
-
- associationHelper - Variable in class etomica.association.MCMoveMoleculeMonomer
-
- associationHelper - Variable in class etomica.association.MCMoveMoleculeRotateAssociated
-
- associationHelper - Variable in class etomica.association.MCMoveMoleculeSmer
-
- associationHelper - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- associationHelper - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- associationHelper - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- associationHelper - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- associationHelper - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- AssociationHelperBranched - Class in etomica.association
-
AssociationHelperBranched is capable of populating a list of atoms in an smer
within a simulation with multiple association sites per atom.
- AssociationHelperBranched(Space, Box, AssociationManager) - Constructor for class etomica.association.AssociationHelperBranched
-
- AssociationHelperDouble - Class in etomica.association
-
AssociationHelperDouble is capable of populating a list of atoms in an smer
within a simulation with double-bonding (two bonding sites per atom).
- AssociationHelperDouble(Space, Box, AssociationManager) - Constructor for class etomica.association.AssociationHelperDouble
-
- AssociationHelperMolecule - Class in etomica.association
-
AssociationHelperBranched is capable of populating a list of molecules in an smer
within a simulation with multiple association sites per molecule.
- AssociationHelperMolecule(Space, Box, AssociationManagerMolecule) - Constructor for class etomica.association.AssociationHelperMolecule
-
- AssociationHelperSingle - Class in etomica.association
-
AssociationHelperSingle is capable of populating a list of atoms in an smer
within a simulation with single-bonding (one bonding site per atom).
- AssociationHelperSingle(AssociationManager) - Constructor for class etomica.association.AssociationHelperSingle
-
- associationManager - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- associationManager - Variable in class etomica.association.AssociationHelperBranched
-
- associationManager - Variable in class etomica.association.AssociationHelperDouble
-
- associationManager - Variable in class etomica.association.AssociationHelperMolecule
-
- associationManager - Variable in class etomica.association.AssociationHelperSingle
-
- AssociationManager - Class in etomica.association
-
Class to define and track atom associations.
- AssociationManager(Box, PotentialMasterCell, AssociationDefinition) - Constructor for class etomica.association.AssociationManager
-
- associationManager - Variable in class etomica.association.AtomSourceRandomDimer
-
- associationManager - Variable in class etomica.association.AtomSourceRandomMonomer
-
- associationManager - Variable in class etomica.association.AtomSourceRandomSmer
-
- associationManager - Variable in class etomica.association.MCMoveAtomDimer
-
- associationManager - Variable in class etomica.association.MCMoveAtomMonomer
-
- associationManager - Variable in class etomica.association.MCMoveAtomNoSmer
-
- associationManager - Variable in class etomica.association.MCMoveAtomSmer
-
- associationManager - Variable in class etomica.association.MCMoveDimer
-
- associationManager - Variable in class etomica.association.MCMoveDimerRotate
-
- associationManager - Variable in class etomica.association.MCMoveMoleculeMonomer
-
- associationManager - Variable in class etomica.association.MCMoveMoleculeRotateAssociated
-
- associationManager - Variable in class etomica.association.MCMoveMoleculeSmer
-
- associationManager - Variable in class etomica.association.MCMoveRotateAssociated
-
- associationManager - Variable in class etomica.association.MCMoveRotateNoSmer
-
- associationManager - Variable in class etomica.association.MCMoveSmer
-
- associationManager - Variable in class etomica.association.MCMoveSmerRotate
-
- associationManager - Variable in class etomica.association.MCMoveVolumeAssociated
-
- associationManager - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- associationManager - Variable in class etomica.association.MoleculeSourceRandomDimer
-
- associationManager - Variable in class etomica.association.MoleculeSourceRandomMonomer
-
- AssociationManagerMolecule - Class in etomica.association
-
Class to define and track molecule associations.
- AssociationManagerMolecule(Simulation, Box, BoxAgentManager<NeighborCellManagerMolecular>, AssociationDefinitionMolecule, double) - Constructor for class etomica.association.AssociationManagerMolecule
-
- associationManagerOriented - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- associationManagerOriented - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- associationManagerOriented - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- associationManagerOriented - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- associationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- associationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- associationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- associationPotential2 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- associationPotential2 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- associationPotential2 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- associationPotential3 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- associationPotential3 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- associationPotential3 - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- asString() - Method in class org.jmol.script.ScriptVariable
-
- asymp(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
-
- asymp(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- at(int) - Method in class etomica.veos.bigdecimal.Bernoulli
-
The Bernoulli number at the index provided.
- at(int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Retrieve a polynomial coefficient.
- at(int) - Method in class etomica.veos.bigdecimal.Euler
-
The Euler number at the index provided.
- at(int) - Method in class etomica.veos.bigdecimal.EulerPhi
-
Compute phi(n).
- at(BigInteger) - Method in class etomica.veos.bigdecimal.EulerPhi
-
Compute phi(n).
- at(int) - Method in class etomica.veos.bigdecimal.Factorial
-
Compute the factorial of the non-negative integer.
- at(int) - Method in class etomica.veos.bigdecimal.Harmonic
-
The Harmonic number at the index specified
- at(int) - Method in class etomica.veos.bigdecimal.PartitionsP
-
return the number of partitions of i
- at(int) - Method in class etomica.veos.bigdecimal.Prime
-
return the ithprime
- atan(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The inverse trigonometric tangent.
- aTarget - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
-
- aTarget - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
-
- aTarget - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
-
- aTarget - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- atom - Variable in class etomica.association.MCMoveDimer
-
- atom - Variable in class etomica.association.MCMoveDimerRotate
-
- atom - Variable in class etomica.association.MCMoveSmer
-
- atom - Variable in class etomica.association.MCMoveSmerRotate
-
- Atom - Class in etomica.atom
-
Atom that represents a physical atom with a position.
- Atom(Space, AtomType) - Constructor for class etomica.atom.Atom
-
- Atom(Space) - Constructor for class etomica.atom.Atom
-
Makes a simple atom for the given space.
- atom - Variable in class etomica.atom.AtomSetSinglet
-
- atom - Variable in class etomica.box.BoxAtomEvent
-
- atom - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- atom - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- atom - Variable in class etomica.integrator.IntegratorHard.Agent
-
- atom() - Method in class etomica.integrator.IntegratorHard.Agent
-
- atom - Variable in class etomica.integrator.mcmove.MCMoveAtom
-
- atom - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- atom - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- atom - Variable in class etomica.models.hexane.MCMoveCBMC
-
- atom - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- atom - Variable in class etomica.molecule.MoleculeSetSinglet
-
- atom - Variable in class etomica.potential.PotentialReactive.BondChangeData
-
- atom - Variable in class etomica.spin.MCMoveSpinFlip
-
- atom - Variable in class etomica.virial.MeterVirialExternalFieldSW.Near
-
- atom0 - Variable in class etomica.atom.AtomPair
-
- atom0 - Variable in class etomica.molecule.MoleculePair
-
- atom0 - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- atom0 - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- atom0 - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- atom0 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- atom1 - Variable in class etomica.association.MCMoveDimer
-
- atom1 - Variable in class etomica.association.MCMoveDimerRotate
-
- atom1 - Variable in class etomica.atom.AtomPair
-
- atom1 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
-
- atom1 - Variable in class etomica.data.DataSourceAtomDistance
-
- atom1 - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- atom1 - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- atom1 - Variable in class etomica.molecule.MoleculePair
-
- atom1 - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- atom1 - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- atom1 - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- atom1 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- ATOM1_INDEX - Static variable in class etomica.util.Debug
-
Atom index of first atom of interest.
- atom2 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
-
- atom2 - Variable in class etomica.data.DataSourceAtomDistance
-
- atom2 - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- atom2 - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- ATOM2_INDEX - Static variable in class etomica.util.Debug
-
Atom index of second atom of interest.
- atom_aC_A - Static variable in class etomica.action.IntegratorDimerApproach
-
- atom_aC_B - Static variable in class etomica.action.IntegratorDimerApproach
-
- atom_aH_A - Static variable in class etomica.action.IntegratorDimerApproach
-
- atom_aH_B - Static variable in class etomica.action.IntegratorDimerApproach
-
- atom_H1_A - Static variable in class etomica.action.IntegratorDimerApproach
-
- ATOM_IN_FRAME - Static variable in class org.jmol.viewer.JmolConstants
-
- atom_O_A - Static variable in class etomica.action.IntegratorDimerApproach
-
- atom_O_B - Static variable in class etomica.action.IntegratorDimerApproach
-
- ATOM_SIZE - Static variable in class etomica.util.Debug
-
The minimum allowable distance between Atoms.
- ATOM_SLABBED - Static variable in class org.jmol.viewer.JmolConstants
-
- AtomAction - Interface in etomica.action
-
Performs an action on an atom.
- AtomActionRandomizeVelocity - Class in etomica.action
-
Action that sets the velocity vector of a given atom to a randomly
chosen value sampled from a Boltzmann distribution.
- AtomActionRandomizeVelocity(double, IRandom) - Constructor for class etomica.action.AtomActionRandomizeVelocity
-
Constructs class to assign velocities according to the given temperature.
- atomActionRandomizeVelocity - Variable in class etomica.action.BoxRandomizeMomenta
-
- atomActionRandomizeVelocity - Variable in class etomica.integrator.IntegratorMD
-
- AtomActionRotateBy - Class in etomica.action
-
Performs RIGHT-HANDED rotations of an atom about the x-, y-, and z-axes by the specified angles (roll, pitch, and yaw angles, respectively) in radians.
- AtomActionRotateBy(Space) - Constructor for class etomica.action.AtomActionRotateBy
-
- atomActionRotateBy - Variable in class etomica.action.IntegratorDimerApproach
-
- AtomActionTransformed - Class in etomica.models.nitrogen
-
Moves (translates) an atom by a specified vector amount.
- AtomActionTransformed(Space) - Constructor for class etomica.models.nitrogen.AtomActionTransformed
-
- AtomActionTransformed - Class in etomica.paracetamol
-
Moves (translates) an atom by a specified vector amount.
- AtomActionTransformed(Space) - Constructor for class etomica.paracetamol.AtomActionTransformed
-
- AtomActionTranslateBy - Class in etomica.action
-
Moves (translates) an atom by a specified vector amount.
- AtomActionTranslateBy(Space) - Constructor for class etomica.action.AtomActionTranslateBy
-
- atomActionTranslateBy - Variable in class etomica.action.IntegratorDimerApproach
-
- atomActionTranslateTo - Variable in class etomica.config.ConfigurationLattice
-
- atomActionTranslateTo - Variable in class etomica.config.ConfigurationLatticeSimple
-
- atomActionTranslateTo - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- atomActionTranslateTo - Variable in class etomica.normalmode.CoordinateDefinition
-
- atomActionTranslateTo - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
- atomActionTranslateTo - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
- AtomAgent(Space) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative.AtomAgent
-
- AtomAgent(Space) - Constructor for class etomica.rotation.IntegratorVelocityVerletQuaternion.AtomAgent
-
- atomAgent0 - Variable in class etomica.dimer.IntegratorDimerMin
-
- atomAgent0 - Variable in class etomica.dimer.IntegratorDimerRT
-
- atomAgent1 - Variable in class etomica.dimer.IntegratorDimerRT
-
- atomAgent2 - Variable in class etomica.dimer.IntegratorDimerRT
-
- atomAgentClass - Variable in class etomica.box.BoxAgentSourceAtomManager
-
- atomAgentManager - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- atomAgentManager - Variable in class etomica.graphics.BondListener
-
- atomAgentManager - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
-
- atomAgentManager - Variable in class etomica.potential.EwaldSummation
-
- atomAgentManager - Variable in class etomica.potential.EwaldSumMolecules
-
- atomAgentManager - Variable in class etomica.potential.P1HarmonicSite
-
- atomAgentManager - Variable in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- atomAgentMin - Variable in class etomica.dimer.IntegratorDimerMin
-
- atomAgentSource - Variable in class etomica.box.BoxAgentSourceAtomManager
-
- atomArray - Variable in class etomica.atom.iterator.TripletInnerSequential
-
- AtomArrayList - Class in etomica.atom
-
- AtomArrayList() - Constructor for class etomica.atom.AtomArrayList
-
- AtomArrayList(int) - Constructor for class etomica.atom.AtomArrayList
-
- atomColor - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- atomCount - Variable in class etomica.modules.entropylottery.MeterEntropy
-
- AtomDecompositionMD - Class in etomica.threads
-
- AtomDecompositionMD() - Constructor for class etomica.threads.AtomDecompositionMD
-
- AtomFilter - Interface in etomica.atom
-
Interface for a class that screens atoms according
to some criterion.
- atomFilter - Variable in class etomica.graphics.DisplayBox
-
- AtomFilterChainLength - Class in etomica.modules.chainequilibrium
-
- AtomFilterChainLength(AtomLeafAgentManager<IAtom[]>) - Constructor for class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- AtomFilterChainLength.LengthAgent - Class in etomica.modules.chainequilibrium
-
- AtomFilterCollective - Interface in etomica.atom
-
Filter that needs to be informed whenever something has changed and the
filtered status of atoms should be redetermined.
- AtomFilterDeviation(ConfigFromFileLAMMPS.ColorSchemeDeviation) - Constructor for class etomica.freeenergy.npath.ConfigFromFileLAMMPS.AtomFilterDeviation
-
- AtomFilterInCylinder(Boundary, P1HardMovingBoundary, double) - Constructor for class etomica.modules.pistoncylinder.ApiFilteredCylinder.AtomFilterInCylinder
-
- AtomFilterLiquid - Class in etomica.modules.droplet
-
- AtomFilterLiquid(Space, IDataSource) - Constructor for class etomica.modules.droplet.AtomFilterLiquid
-
- AtomFilterLiquidAtomic - Class in etomica.modules.droplet
-
- AtomFilterLiquidAtomic(PotentialMasterList, Box) - Constructor for class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- atomGroupAction - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- atomGroupAction - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- atomGroupAction - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- atomGroupAction - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- atomGroupAction - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- atomGroupAction - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- atomGroupAction - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- atomGroupAction - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
- atomGroupAction - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
- atomGroupAction - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- atomGroupActionRotateBy - Variable in class etomica.action.IntegratorDimerApproach
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- atomGroupActionTranslate - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- atomGroupActionTranslateBy - Variable in class etomica.action.IntegratorDimerApproach
-
- AtomGroupVelocityAverage - Class in etomica.atom
-
Calculates the mass average velocity over a set of atoms.
- AtomGroupVelocityAverage(Space) - Constructor for class etomica.atom.AtomGroupVelocityAverage
-
- AtomHydrogen - Class in etomica.atom
-
- AtomHydrogen(Space, AtomTypeOriented, double) - Constructor for class etomica.atom.AtomHydrogen
-
- atomicMass - Static variable in class org.jmol.util.Elements
-
- atomicNumber - Variable in class etomica.chem.elements.ElementChemical
-
- atomicPotentials - Variable in class etomica.potential.PotentialMasterLrc
-
- atomicTensor(IAtom, IAtom) - Method in interface etomica.models.water.P2Water4PSoft.AtomicTensorAtomicPair
-
- atomicTensor(IAtom, IAtom) - Method in interface etomica.normalmode.LatticeSumMolecularCrystal.AtomicTensorAtomicPair
-
- atomicTensorAtomicPair - Variable in class etomica.normalmode.NormalModesMolecular
-
- atomicToMolecularD(IMolecule, IMolecule) - Method in class etomica.models.water.P2Water4PSoft
-
- atomicToMolecularD(LatticeSumMolecularCrystal.AtomicTensorAtomicPair, IMolecule, IMolecule) - Method in class etomica.normalmode.LatticeSumMolecularCrystal
-
- atomid - Static variable in class org.jmol.script.Token
-
- ATOMID_ALPHA_CARBON - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_ALPHA_ONLY_MASK - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_AMINO_NITROGEN - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_C1_PRIME - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_C2 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_C3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_C4 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_C4_PRIME - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_C5 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_C5M - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_C6 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_C7 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_C8 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_CARBONYL_CARBON - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_CARBONYL_OD1 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_CARBONYL_OD2 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_CARBONYL_OE1 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_CARBONYL_OE2 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_CARBONYL_OXYGEN - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_DISTINGUISHING_ATOM_MAX - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_H3T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_H5T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_HO3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_HO5_PRIME - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_MAX - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_N1 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_N2 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_N3 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_N4 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_N6 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_N7 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_N9 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_NUCLEIC_MASK - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_NUCLEIC_PHOSPHORUS - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_O1 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_O1P - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_O2 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_O2_PRIME - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_O2P - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_O3_PRIME - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_O4 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_O5_PRIME - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_O5T_TERMINUS - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_O6 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_OP1 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_OP2 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_PHOSPHORUS_ONLY_MASK - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_PROTEIN_MASK - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_S4 - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_SG - Static variable in class org.jmol.viewer.JmolConstants
-
- ATOMID_TERMINATING_OXT - Static variable in class org.jmol.viewer.JmolConstants
-
- atomindex - Static variable in class org.jmol.script.Token
-
- AtomIterator - Interface in etomica.atom.iterator
-
Interface for classes that loop over a set of atoms.
- atomIterator - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- atomIterator - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- atomIterator - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- atomIterator - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- atomIterator - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- AtomIterator0() - Constructor for class etomica.potential.PotentialMaster.AtomIterator0
-
- AtomIteratorAllLeafType - Class in etomica.atom.iterator
-
Iterator for all the molecules of a set of species in a box.
- AtomIteratorAllLeafType(AtomType[]) - Constructor for class etomica.atom.iterator.AtomIteratorAllLeafType
-
- AtomIteratorArrayList - Class in etomica.atom.iterator
-
An atom iterator of the elements from an AtomArrayList (in proper
sequence).
- AtomIteratorArrayList(IteratorDirective.Direction) - Constructor for class etomica.atom.iterator.AtomIteratorArrayList
-
Constructs new iterator with an empty list.
- AtomIteratorArrayList(IteratorDirective.Direction, int) - Constructor for class etomica.atom.iterator.AtomIteratorArrayList
-
Constructs new iterator set to iterate given list (upon reset).
- AtomIteratorArrayList(IteratorDirective.Direction, int, AtomToIndex, AtomToAtomLeafList) - Constructor for class etomica.atom.iterator.AtomIteratorArrayList
-
- AtomIteratorArrayListAdjacent - Class in etomica.atom.iterator
-
Returns one or both of the atoms adjacent to a specified atom in
its parent's child list.
- AtomIteratorArrayListAdjacent(IteratorDirective.Direction) - Constructor for class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
Constructor gives iterator not ready for iteration.
- AtomIteratorArrayListAdjacent(IteratorDirective.Direction, AtomToIndex, AtomToAtomLeafList) - Constructor for class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
- AtomIteratorArrayListSimple - Class in etomica.atom.iterator
-
An atom iterator of the elements from an AtomArrayList (in proper
sequence).
- AtomIteratorArrayListSimple() - Constructor for class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Constructs new iterator with an empty list.
- AtomIteratorArrayListSimple(IAtomList) - Constructor for class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Constructs new iterator set to iterate given list (upon reset).
- AtomIteratorAtomDependent - Interface in etomica.atom.iterator
-
Interface for an atom iterator that can be altered by setting
of an atom.
- AtomIteratorBasis - Class in etomica.atom.iterator
-
Elementary basis-dependent iterator that gives atoms meeting specification
of a basis and a target.
- AtomIteratorBasis() - Constructor for class etomica.atom.iterator.AtomIteratorBasis
-
Constructor makes iterator in an unset condition; must set basis and call reset before
beginning iteration.
- AtomIteratorBasisAdjustableStart - Class in etomica.atom.iterator
-
Elementary basis-dependent iterator that gives atoms meeting specification
of a basis and a target.
- AtomIteratorBasisAdjustableStart() - Constructor for class etomica.atom.iterator.AtomIteratorBasisAdjustableStart
-
Constructor makes iterator in an unset condition; must set basis and call reset before
beginning iteration.
- AtomIteratorBasisDependent - Interface in etomica.atom.iterator
-
- AtomIteratorBasisFilteredType - Class in etomica.atom.iterator
-
- AtomIteratorBasisFilteredType(AtomType) - Constructor for class etomica.atom.iterator.AtomIteratorBasisFilteredType
-
- AtomIteratorBasisFilteredType2 - Class in etomica.atom.iterator
-
This iterator returns atoms that are one of two types.
- AtomIteratorBasisFilteredType2(AtomType, AtomType) - Constructor for class etomica.atom.iterator.AtomIteratorBasisFilteredType2
-
- AtomIteratorBoxDependent - Interface in etomica.atom.iterator
-
Interface indicating that an atom iterator can determine appropriate
atoms for iteration given an arbitrary box.
- AtomIteratorBruteForce(Box) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- AtomIteratorCell - Class in etomica.nbr.cell
-
Returns occupants of all cells as iterates.
- AtomIteratorCell(int, BoxAgentManager) - Constructor for class etomica.nbr.cell.AtomIteratorCell
-
Constructor makes iterator that must have box specified and then be
reset() before iteration.
- AtomIteratorLeafAtoms - Class in etomica.atom.iterator
-
Iterator that will loop over all leaf atoms in a box.
- AtomIteratorLeafAtoms() - Constructor for class etomica.atom.iterator.AtomIteratorLeafAtoms
-
Creates iterator with no box specified.
- AtomIteratorLeafAtoms(Box) - Constructor for class etomica.atom.iterator.AtomIteratorLeafAtoms
-
Creates iterator conditioned to give all leaf atoms of the specified
box.
- AtomIteratorLeafFilteredType - Class in etomica.atom.iterator
-
- AtomIteratorLeafFilteredType(Box, AtomType) - Constructor for class etomica.atom.iterator.AtomIteratorLeafFilteredType
-
- AtomIteratorNbr(NeighborListManager) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- AtomIteratorNbrCell(double, BoxAgentManager<? extends BoxCellManager>, Box) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- AtomIteratorNull - Class in etomica.atom.iterator
-
Static iterator that returns no atoms.
- AtomIteratorSinglet - Class in etomica.atom.iterator
-
Iterator that expires after returning a single atom, which is
specified by a call to the setAtom method, or via the constructor.
- AtomIteratorSinglet() - Constructor for class etomica.atom.iterator.AtomIteratorSinglet
-
Constructs iterator without defining atom.
- AtomIteratorSinglet(IAtom) - Constructor for class etomica.atom.iterator.AtomIteratorSinglet
-
Constructs iterator specifying that it return the given atom.
- atomLeafAgentManager - Variable in class etomica.association.MCMoveVolumeAssociated
-
- AtomLeafAgentManager<E> - Class in etomica.atom
-
AtomAgentManager acts on behalf of client classes (an AgentSource) to
manage agents for every leaf Atom in a box.
- AtomLeafAgentManager(AtomLeafAgentManager.AgentSource<E>, Box) - Constructor for class etomica.atom.AtomLeafAgentManager
-
- AtomLeafAgentManager.AgentSource<E> - Interface in etomica.atom
-
Interface for an object that wants an agent associated with each Atom in
a Box.
- AtomLeafDynamic - Class in etomica.atom
-
- AtomLeafDynamic(Space, AtomType) - Constructor for class etomica.atom.AtomLeafDynamic
-
- atomLeafIndexChanged(IAtom, int) - Method in class etomica.box.BoxEventManager
-
- AtomLeafsetIterator - Interface in etomica.atom.iterator
-
Interface for classes that loop over a set of atoms.
- atomList - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- atomList - Variable in class etomica.data.meter.MeterStructureFactor
-
- atomList - Variable in class etomica.models.hexane.MCMoveCBMC
-
- AtomListProperty - Class in etomica.meta.properties
-
Created by kofke on 7/24/17.
- AtomListProperty(Object, PropertyDescriptor) - Constructor for class etomica.meta.properties.AtomListProperty
-
- atomLists - Variable in class etomica.atom.iterator.ANIntergroupCoupled
-
- AtomListWrapper - Class in etomica.atom
-
AtomSet formed by wrapping an AtomArrayList.
- AtomListWrapper() - Constructor for class etomica.atom.AtomListWrapper
-
Wraps a new atom array of the given length.
- AtomListWrapper(IAtomList) - Constructor for class etomica.atom.AtomListWrapper
-
Makes a new instance holding the atoms in the given atom set.
- AtomListWrapper(AtomArrayList) - Constructor for class etomica.atom.AtomListWrapper
-
Wraps the given atom array.
- atomMove - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- atomMove - Variable in class etomica.normalmode.SimEinStep1
-
- atomMove - Variable in class etomica.normalmode.SimEinStep1HCP
-
- atomMove - Variable in class etomica.normalmode.SimEinStep2
-
- atomMove - Variable in class etomica.normalmode.SimEinStep2HCP
-
- atomMove - Variable in class etomica.normalmode.SimLJHTTISuper
-
- atomMove - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- atomMove - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- atomMove - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- atomMoveRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- atomMoveTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- atomname - Static variable in class org.jmol.script.Token
-
- AtomNeighborLists - Class in etomica.nbr.list
-
Class used to maintain neighbor lists.
- AtomNeighborLists() - Constructor for class etomica.nbr.list.AtomNeighborLists
-
Constructs sequencer for the given atom.
- atomno - Static variable in class org.jmol.script.Token
-
- atomNumber - Variable in class etomica.modules.materialfracture.StrainColorScheme
-
- atomNumberMod - Variable in class etomica.modules.materialfracture.StrainColorScheme
-
- AtomOriented - Class in etomica.atom
-
- AtomOriented(Space, AtomType) - Constructor for class etomica.atom.AtomOriented
-
- AtomOriented(Space, AtomType, boolean) - Constructor for class etomica.atom.AtomOriented
-
- AtomOrientedDynamic - Class in etomica.atom
-
- AtomOrientedDynamic(Space, AtomType) - Constructor for class etomica.atom.AtomOrientedDynamic
-
- AtomOrientedDynamic(Space, AtomType, boolean) - Constructor for class etomica.atom.AtomOrientedDynamic
-
- AtomOrientedQuaternion - Class in etomica.atom
-
- AtomOrientedQuaternion(Space, AtomType) - Constructor for class etomica.atom.AtomOrientedQuaternion
-
- AtomPair - Class in etomica.atom
-
Data structure that contains two mutable atom instances.
- AtomPair() - Constructor for class etomica.atom.AtomPair
-
- AtomPair(IAtom, IAtom) - Constructor for class etomica.atom.AtomPair
-
- atomPair - Variable in class etomica.nbr.list.PotentialMasterList
-
- atomPair - Variable in class etomica.potential.PotentialMasterMonatomic
-
- atomPair - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- atomPair - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- AtomPairSet - Class in etomica.virial
-
Class that holds a set of atom pairs.
- AtomPairSet(IMoleculeList) - Constructor for class etomica.virial.AtomPairSet
-
Constructor for AtomPairSet.
- atompicking - Static variable in class org.jmol.script.Token
-
- atomPosDef - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
-
- atomPositionCOM - Variable in class etomica.integrator.IntegratorRigidIterative
-
- atomPositionCOM - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- atomPositionCOM - Variable in class etomica.models.water.OrientationCalcWater3P
-
- atomPositionCOM - Variable in class etomica.models.water.OrientationCalcWater4P
-
- atomPositionCOM - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- AtomPotential1ListSource(PotentialMasterList) - Constructor for class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
-
- AtomPotentialList - Class in etomica.nbr.list
-
Class used to maintain list of whether each 1-body potential that applies to an AtomType is currently in effect or
not for an Atom.
- AtomPotentialList() - Constructor for class etomica.nbr.list.AtomPotentialList
-
Constructs sequencer for the given atom.
- atomproperty - Static variable in class org.jmol.script.Token
-
- atoms - Variable in class etomica.atom.iterator.ANIntergroupCoupled
-
- atoms - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- atoms - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- atoms - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- atoms - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- atoms - Variable in class etomica.potential.PotentialMolecularMonatomic
-
- atoms - Variable in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- atoms - Variable in class etomica.virial.CoordinatePairMoleculeSet
-
- atoms - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- atoms - Variable in class etomica.virial.MCMoveClusterRingScale
-
- atoms - Static variable in class org.jmol.script.Token
-
- Atomset3IteratorIndexList - Class in etomica.atom.iterator
-
Atomset Iterator that iterates over set-of-three atoms
- Atomset3IteratorIndexList(int[][]) - Constructor for class etomica.atom.iterator.Atomset3IteratorIndexList
-
Constructs iterator without defining set of atoms.
- Atomset4IteratorIndexList - Class in etomica.atom.iterator
-
Atomset Iterator that iterates over set-of-four atoms
- Atomset4IteratorIndexList(int[][]) - Constructor for class etomica.atom.iterator.Atomset4IteratorIndexList
-
Constructs iterator without defining set of atoms.
- atomSetA - Variable in class etomica.action.IntegratorDimerApproach
-
- AtomSetAllMolecules - Class in etomica.box
-
Creates a facade that makes a set of molecule lists look like a single list.
- AtomSetAllMolecules() - Constructor for class etomica.box.AtomSetAllMolecules
-
Constructs an empty list.
- AtomsetArray - Class in etomica.atom
-
AtomSet formed by wrapping an Atom array.
- AtomsetArray(int) - Constructor for class etomica.atom.AtomsetArray
-
Wraps a new atom array of the given length.
- AtomsetArray(IAtomList) - Constructor for class etomica.atom.AtomsetArray
-
Makes a new instance holding the atoms in the given atom set.
- AtomsetArray(AtomsetArray) - Constructor for class etomica.atom.AtomsetArray
-
Copy constructor, wrapping a new array unique to this instance but
holding the same atoms as the given atom set.
- AtomsetArray(IAtom[]) - Constructor for class etomica.atom.AtomsetArray
-
Wraps the given atom array.
- atomsetArrayList - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- atomsetArrayList - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- atomSetB - Variable in class etomica.action.IntegratorDimerApproach
-
- AtomsetIterator - Interface in etomica.atom.iterator
-
Interface for classes that loop over a set of atoms.
- AtomsetIteratorAllLeafAtoms - Class in etomica.atom.iterator
-
Iterator for all the molecules of a set of species in a box.
- AtomsetIteratorAllLeafAtoms() - Constructor for class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
- AtomsetIteratorBasisDependent - Interface in etomica.atom.iterator
-
Interface for an AtomIterator that can be conditioned with
target and basis atoms.
- AtomsetIteratorBoxDependent - Interface in etomica.atom.iterator
-
Interface indicating that an iterator can determine appropriate
atoms for iteration given an arbitrary box.
- AtomsetIteratorCellular - Interface in etomica.nbr.cell
-
Interface for atomset iterators that use cell-based neighbor
lists for iteration.
- AtomsetIteratorDirectable - Interface in etomica.atom.iterator
-
Interface for an iterator that can interpret specification of
direction UP or DOWN.
- AtomsetIteratorPDT - Interface in etomica.atom.iterator
-
This is an interface for iterators that are box dependent, directable,
and targetable.
- AtomsetIteratorTargetable - Interface in etomica.atom.iterator
-
Interface for an iterator that can be targeted at one or more atoms.
- AtomSetSinglet - Class in etomica.atom
-
Data structure that contains a single mutable atom instance.
- AtomSetSinglet() - Constructor for class etomica.atom.AtomSetSinglet
-
- AtomSetSinglet(IAtom) - Constructor for class etomica.atom.AtomSetSinglet
-
- atomSetSinglet - Variable in class etomica.atom.iterator.ApiIntergroup
-
- atomSetSinglet - Variable in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
- atomSetSinglet - Variable in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
- atomSetSinglet - Variable in class etomica.atom.iterator.AtomIteratorSinglet
-
- atomSetSinglet - Variable in class etomica.freeenergy.npath.IntegratorImageMultistepMD
-
- atomSetSinglet - Variable in class etomica.graphics.BondListener
-
- atomSetSinglet - Variable in class etomica.integrator.IntegratorHard.Agent
-
- atomSetSinglet - Variable in class etomica.modules.pistoncylinder.IntegratorHardPiston
-
- atomSetSinglet - Variable in class etomica.molecule.iterator.MoleculeIteratorArrayListSimple
-
- atomSetSinglet - Variable in class etomica.molecule.iterator.MoleculeIteratorSinglet
-
- atomSetSinglet - Variable in class etomica.nbr.cell.AtomIteratorCell
-
- atomSetSinglet - Variable in class etomica.nbr.list.NeighborListManager
-
- atomSetSinglet - Variable in class etomica.nbr.list.PotentialMasterList
-
- atomSetSinglet - Variable in class etomica.nbr.PotentialGroupNbr
-
- atomSetSinglet - Variable in class etomica.nbr.site.PotentialMasterSite
-
- atomSetSinglet - Variable in class etomica.potential.PotentialMasterMonatomic
-
- atomSetSinglet - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- atomSetSinglet - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- atomSinglet - Variable in class etomica.freeenergy.npath.MCMoveAtomNPath
-
- atomSinglet - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- AtomSite - Class in etomica.nbr.site
-
Site used to form array of cells for cell-based neighbor listing.
- AtomSite(int) - Constructor for class etomica.nbr.site.AtomSite
-
- atomSource - Variable in class etomica.association.MCMoveDimer
-
- atomSource - Variable in class etomica.association.MCMoveDimerRotate
-
- atomSource - Variable in class etomica.association.MCMoveSmer
-
- atomSource - Variable in class etomica.association.MCMoveSmerRotate
-
- AtomSource - Interface in etomica.atom
-
Interface for objects when return atoms (meeting some specification)
from a box.
- atomSource - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- atomSource - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- atomSource - Variable in class etomica.integrator.mcmove.MCMoveAtom
-
- atomSource - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- atomSource - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- atomSource - Variable in class etomica.models.hexane.MCMoveReptate
-
- atomSource - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- atomSource - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- atomSource - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- atomSource - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- AtomSourceRandomDimer - Class in etomica.association
-
- AtomSourceRandomDimer() - Constructor for class etomica.association.AtomSourceRandomDimer
-
- AtomSourceRandomLeaf - Class in etomica.atom
-
AtomSource that returns a completely random leaf atom.
- AtomSourceRandomLeaf() - Constructor for class etomica.atom.AtomSourceRandomLeaf
-
- AtomSourceRandomMonomer - Class in etomica.association
-
- AtomSourceRandomMonomer() - Constructor for class etomica.association.AtomSourceRandomMonomer
-
- AtomSourceRandomSmer - Class in etomica.association
-
- AtomSourceRandomSmer() - Constructor for class etomica.association.AtomSourceRandomSmer
-
- AtomSourceRandomSpecies - Class in etomica.atom
-
AtomSource that returns a completely random leaf atom.
- AtomSourceRandomSpecies() - Constructor for class etomica.atom.AtomSourceRandomSpecies
-
- AtomSourceRandomSpecies(IRandom, ISpecies) - Constructor for class etomica.atom.AtomSourceRandomSpecies
-
- atomSpeciesA - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- atomSpeciesB - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- atomsPerGroup - Variable in class etomica.species.SpeciesSpheres
-
- AtomTag() - Constructor for class etomica.modules.chainequilibrium.MeterChainLength.AtomTag
-
- AtomTimeAction() - Constructor for class etomica.integrator.IntegratorAnalytic.AtomTimeAction
-
- AtomToAtomLeafList - Interface in etomica.atom
-
Interface for class that determines an AtomArrayList given an atom.
- atomToAtomSet - Variable in class etomica.molecule.iterator.MpiIntraspecies1A
-
- AtomToAtomSetFixed - Class in etomica.atom
-
- AtomToAtomSetFixed() - Constructor for class etomica.atom.AtomToAtomSetFixed
-
- AtomToIndex - Interface in etomica.atom
-
Interface for class that associates an integer with an atom.
- AtomToIndexChild - Class in etomica.atom
-
Defines the index as the Atom's node's index.
- AtomToIndexChild() - Constructor for class etomica.atom.AtomToIndexChild
-
- AtomToParentChildList - Class in etomica.atom
-
- AtomToParentChildList() - Constructor for class etomica.atom.AtomToParentChildList
-
- atomToPosVec(IAtom) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- atomTranslator - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
-
- atomTranslator - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- AtomType - Class in etomica.atom
-
Identifies a set of atoms and defines properties of those atoms.
- AtomType(IElement) - Constructor for class etomica.atom.AtomType
-
- atomType - Variable in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
-
- atomtype - Static variable in class org.jmol.script.Token
-
- AtomTypeAgentManager<E> - Class in etomica.atom
-
AtomTypeAgentManager acts on behalf of client classes (an AgentSource) to manage agents for every AtomType in a box.
- AtomTypeAgentManager(AtomTypeAgentManager.AgentSource<E>, Simulation) - Constructor for class etomica.atom.AtomTypeAgentManager
-
- AtomTypeAgentManager.AgentSource<E> - Interface in etomica.atom
-
Interface for an object that wants an agent associated with each AtomType in a Simulation.
- atomTypeIndexChanged(AtomType, int) - Method in class etomica.simulation.SimulationEventManager
-
- atomTypeMaxIndexChanged(int) - Method in class etomica.simulation.SimulationEventManager
-
- AtomTypeOriented - Class in etomica.atom
-
Atom type for a sphere that has some feature depending upon an orientation coordinate.
- AtomTypeOriented(IElement, Space) - Constructor for class etomica.atom.AtomTypeOriented
-
Deprecated.
- AtomTypeOriented(IElement, Vector) - Constructor for class etomica.atom.AtomTypeOriented
-
- atomTypeOrientedManager - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- atomTypes - Variable in class etomica.potential.P2SquareWellRobust
-
- atomTypes - Variable in class etomica.species.Species
-
- atomtypes - Static variable in class org.jmol.script.Token
-
- AtomTypeSpheroPolyhedron - Class in etomica.atom
-
- AtomTypeSpheroPolyhedron(IElement, Space, List<Vector>, double) - Constructor for class etomica.atom.AtomTypeSpheroPolyhedron
-
- atomx - Static variable in class org.jmol.script.Token
-
- atomy - Static variable in class org.jmol.script.Token
-
- atomz - Static variable in class org.jmol.script.Token
-
- auto - Static variable in class org.jmol.script.Token
-
- autobond - Static variable in class org.jmol.script.Token
-
- autofps - Static variable in class org.jmol.script.Token
-
- autoRowLabels - Variable in class etomica.graphics.DisplayTable
-
- aveCosTheta - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- AVERAGE - Static variable in class etomica.data.AccumulatorAverage
-
- average - Variable in class etomica.data.AccumulatorAverage
-
- AVERAGE - Static variable in class etomica.data.AccumulatorAverageBlockless
-
- average - Variable in class etomica.data.AccumulatorAverageBlockless
-
- AVERAGE - Static variable in class etomica.data.AccumulatorAverageBlocklessSlim
-
- average - Static variable in class org.jmol.script.Token
-
- averageBox - Variable in class etomica.graphics.DisplayTextBoxesCAE
-
- averages - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- averages - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- AVG - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- AVG - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- avg - Variable in class etomica.modules.statistics.StatisticsMCGraphic.HistoryPlotBits
-
- avgEnergy - Variable in class etomica.simulation.prototypes.LJMD3D
-
- avgEnergy - Variable in class etomica.thermointegration.LjMc3D
-
- avgStat - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- AVOGADRO - Static variable in class etomica.util.Constants
-
Avogadro's number, 6.022140857(74)e23 molecules/mole.
- axes - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- axes - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- AXES - Static variable in class g3dsys.control.G3DSys
-
- Axes - Class in g3dsys.images
-
- Axes(G3DSys, short) - Constructor for class g3dsys.images.Axes
-
- axes - Static variable in class org.jmol.script.Token
-
- AXES_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
-
- axescolor - Static variable in class org.jmol.script.Token
-
- axesmode - Static variable in class org.jmol.script.Token
-
- axesmolecular - Static variable in class org.jmol.script.Token
-
- axesorientationrasmol - Static variable in class org.jmol.script.Token
-
- axesscale - Static variable in class org.jmol.script.Token
-
- axesTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- axesunitcell - Static variable in class org.jmol.script.Token
-
- axeswindow - Static variable in class org.jmol.script.Token
-
- axis - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- axis - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- axis - Variable in class etomica.models.nitrogen.TestRotationVector
-
- axis - Variable in class etomica.modules.droplet.AtomFilterLiquid
-
- axis - Variable in class etomica.modules.droplet.ConfigurationDroplet
-
- axis - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- axis - Variable in class etomica.virial.ClusterCoupledAtomFlipped
-
- axis - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- axis - Static variable in class org.jmol.script.Token
-
- axis0 - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- axis0 - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- axis0Prime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- axis1color - Static variable in class org.jmol.script.Token
-
- axis2color - Static variable in class org.jmol.script.Token
-
- axis3color - Static variable in class org.jmol.script.Token
-
- AxisAngle4f - Class in org.jmol.util
-
A 4 element axis angle represented by single precision floating point
x,y,z,angle components.
- AxisAngle4f() - Constructor for class org.jmol.util.AxisAngle4f
-
Constructs and initializes a AxisAngle4f to (0,0,1,0).
- axisNorm - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- axisNormPrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- axisNX - Static variable in class org.jmol.viewer.JmolConstants
-
- axisNY - Static variable in class org.jmol.viewer.JmolConstants
-
- axisNZ - Static variable in class org.jmol.viewer.JmolConstants
-
- axisX - Static variable in class org.jmol.viewer.JmolConstants
-
- axisY - Static variable in class org.jmol.viewer.JmolConstants
-
- axisZ - Static variable in class org.jmol.viewer.JmolConstants
-
- B - Variable in class etomica.conjugategradient.ConjugateGradients
-
- B - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- B - Variable in class etomica.conjugategradient.SteepestDescent
-
- b - Variable in class etomica.dimer.P1LepsHarmonic
-
- b - Variable in class etomica.math.numerical.PadeApproximation
-
- B - Variable in class etomica.meam.PotentialCuLREP
-
- B - Variable in class etomica.meam.PotentialEFS
-
- b - Variable in class etomica.models.co2.P2CO2Hellmann
-
- b - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- b - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- B - Variable in class etomica.potential.P2HePCKLJS
-
- b - Static variable in class etomica.potential.P2HePCKLJS
-
- b - Variable in class etomica.potential.P2NitrogenHellmann
-
- b - Variable in class etomica.potential.P2WaterPotentialsJankowski
-
- B - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- b - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- b - Variable in class etomica.potential.P3HydrogenManzhos
-
- b0 - Variable in class etomica.meam.ParameterSetMEAM
-
- b1 - Variable in class etomica.meam.ParameterSetMEAM
-
- B1 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- B1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- B1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- B10HS(double) - Static method in class etomica.virial.cluster.Standard
-
- B11HS(double) - Static method in class etomica.virial.cluster.Standard
-
- B12HS(double) - Static method in class etomica.virial.cluster.Standard
-
- b2 - Variable in class etomica.meam.ParameterSetMEAM
-
- B2 - Variable in class etomica.modules.adsorption.VEOS3SW
-
- B2(double, double) - Static method in class etomica.modules.vle.LJQB2
-
Returns B2 for the LJ+quadrupole model.
- B2(double) - Static method in class etomica.statmech.LennardJones
-
Returns the 2nd virial coefficient.
- B2 - Static variable in class etomica.virial.cluster.Standard
-
- B2 - Variable in class etomica.virial.simulations.ShapeParser.ShapeData
-
- B2Fit - Class in etomica.modules.vle
-
- B2Fit() - Constructor for class etomica.modules.vle.B2Fit
-
- B2Fit.Applet - Class in etomica.modules.vle
-
- B2Fit.FunctionB2LJQ - Class in etomica.modules.vle
-
Function using LJQB2 to evaluate B2 as a function of Q, epsilon, sigma
and T.
- B2Fit.FunctionMayerB2LJQ - Class in etomica.modules.vle
-
Function using Mayer sampling to evaluate B2 as a function of Q,
epsilon, sigma and T.
- B2ForSphericallySymmetricUByTrapezoidRule - Class in etomica.virial
-
- B2ForSphericallySymmetricUByTrapezoidRule() - Constructor for class etomica.virial.B2ForSphericallySymmetricUByTrapezoidRule
-
- B2Hash - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
-
- B2HS(double) - Static method in class etomica.virial.cluster.Standard
-
- B2Ionic - Class in etomica.virial
-
two points cluster diagrams calculation
Integral I2,S2,mean activity coefficient,osmotic coefficient of ionic solution via single integrals
include cycle diagram(=>DHLL); (k0); (k2);(kn+n)
=0, k-bond, =1, modified q-bond,etc, m>3,two diagrams are added up to evaluate
s = parameter * c^2 * I
ds/dc = parameter * ( 2*c*I + c^2 * dI/dc)
all are in simulation units
contains "linear step in sqrt(c)" && "linear step in c"
- B2Ionic() - Constructor for class etomica.virial.B2Ionic
-
- B2SW(double, double, double) - Static method in class etomica.virial.cluster.Standard
-
- b3 - Variable in class etomica.meam.ParameterSetMEAM
-
- B3 - Variable in class etomica.modules.adsorption.VEOS3SW
-
- B3ForSphericallySymmetricU - Class in etomica.virial
-
Compute B3 for a spherically symmetric potential to within a given tolerance, specified with getConvergece(), by
either FFT or FFT and one layer of quadrature.
- B3ForSphericallySymmetricU() - Constructor for class etomica.virial.B3ForSphericallySymmetricU
-
- B3ForSphericallySymmetricU.DampingParams - Class in etomica.virial
-
- B3HS(double) - Static method in class etomica.virial.cluster.Standard
-
- B3LJ - Class in etomica.virial
-
This is a main method to compute B3 and dB3/dT for Lennard-Jones via FFT
It creates a discretization of the Lennard-Jones Mayer function, and computes
B3 via FFT.
- B3LJ() - Constructor for class etomica.virial.B3LJ
-
- B3NonAddForSphericallySymmetricU - Class in etomica.virial
-
Computes the classical, non-additive component of B3 for a spherically symmetric potential using quadrature.
- B3NonAddForSphericallySymmetricU() - Constructor for class etomica.virial.B3NonAddForSphericallySymmetricU
-
- B3SW(double, double, double) - Static method in class etomica.virial.cluster.Standard
-
- b45 - Variable in class etomica.modules.sam.P1Sinusoidal
-
- B4FFTLJ - Class in etomica.virial
-
Computes four approximations of B4 by FFT: HNC(C), HNC(V), PY(C), and PY(V).
- B4FFTLJ() - Constructor for class etomica.virial.B4FFTLJ
-
- B4HS(double) - Static method in class etomica.virial.cluster.Standard
-
- B5FFTLJ - Class in etomica.virial
-
Computes four approximations of B5 by FFT: HNC(C), HNC(V), PY(C), and PY(V).
- B5FFTLJ() - Constructor for class etomica.virial.B5FFTLJ
-
- B5HS(double) - Static method in class etomica.virial.cluster.Standard
-
- B6FFTLJ - Class in etomica.virial
-
Modification of FFT Program of B4
- B6FFTLJ() - Constructor for class etomica.virial.B6FFTLJ
-
- B6HS(double) - Static method in class etomica.virial.cluster.Standard
-
- B7HS(double) - Static method in class etomica.virial.cluster.Standard
-
- B8HS(double) - Static method in class etomica.virial.cluster.Standard
-
- B9HS(double) - Static method in class etomica.virial.cluster.Standard
-
- bA - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- bA - Static variable in class etomica.potential.P2NitrogenHellmann
-
- backbone - Static variable in class org.jmol.script.Token
-
- backgroundColor - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Background color for the output images.
- backgroundcolor - Static variable in class org.jmol.script.Token
-
- backgroundImage - Variable in class org.jmol.util.GData
-
- backgroundmodel - Static variable in class org.jmol.script.Token
-
- backlit - Static variable in class org.jmol.script.Token
-
- backTrack() - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- backTrack() - Method in interface etomica.graph.isomorphism.SearchState
-
- backTrack() - Method in class etomica.graph.isomorphism.VF2SearchState
-
- backTrack() - Method in class etomica.graph.isomorphism.VFSearchState
-
- backwardDataMap - Variable in class etomica.data.DataSet
-
- bALattice - Variable in class etomica.normalmode.DataSourceMuRoot1
-
- bALattice - Variable in class etomica.normalmode.DataSourceMuRootPMatch
-
- bALattice - Variable in class etomica.normalmode.DataSourcePMu
-
- BALL - Static variable in class g3dsys.control.G3DSys
-
implemented shapes
- Ball - Class in g3dsys.images
-
Class for drawing spheres (atoms)
- Ball(G3DSys, short, float, float, float, float) - Constructor for class g3dsys.images.Ball
-
- Ball(G3DSys, short, Point3f, float) - Constructor for class g3dsys.images.Ball
-
- Bar - Class in etomica.units
-
The bar unit of pressure, equal to 10^5 N/m^2.
- Barye - Class in etomica.units
-
The barye unit of pressure, equal to 1 dyn/cm^2.
- baseline() - Method in class etomica.space.BenchVector3D
-
- basepair - Static variable in class org.jmol.script.Token
-
- baseUnits() - Method in class etomica.units.systems.UnitSystem
-
Base dimensions are {length, mass, time, current, temperature, quantity, luminous intensity}
- BasicHealthCheck - Class in etomica.server.health
-
- BasicHealthCheck() - Constructor for class etomica.server.health.BasicHealthCheck
-
- basis - Variable in class etomica.lattice.BravaisLatticeCrystal
-
- Basis - Class in etomica.lattice.crystal
-
General basis class that hold scaled coordinates of atoms within a unit cell.
- Basis(Vector[]) - Constructor for class etomica.lattice.crystal.Basis
-
- basis - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- basis - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- basis - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- basis - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
-
- basis - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
-
- basis - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
-
- basis - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- basis - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- basis - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- basis - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- basis - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- basis - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- basis - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
-
- basis - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- basis - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- basis - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- basis - Variable in class etomica.models.oneDHardRods.SimWidomMode
-
- basis - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- basis - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- basis - Variable in class etomica.normalmode.CoordinateDefinition
-
- basis - Variable in class etomica.normalmode.HessianDB
-
- basis - Variable in class etomica.normalmode.LJVacancyMin
-
- basis - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- basis - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- basis - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- basis - Variable in class etomica.normalmode.NormalModes2D
-
- basis - Variable in class etomica.normalmode.NormalModes3D
-
- basis - Variable in class etomica.normalmode.SimBennet
-
- basis - Variable in class etomica.normalmode.SimCalcSLJ
-
- basis - Variable in class etomica.normalmode.SimCalcSMorse
-
- basis - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
-
- basis - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- basis - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- basis - Variable in class etomica.normalmode.SimEinStep1
-
- basis - Variable in class etomica.normalmode.SimEinStep1HCP
-
- basis - Variable in class etomica.normalmode.SimEinStep2
-
- basis - Variable in class etomica.normalmode.SimEinStep2HCP
-
- basis - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- basis - Variable in class etomica.normalmode.SimLJHTTISuper
-
- basis - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- basis - Variable in class etomica.normalmode.SimOverlap
-
- basis - Variable in class etomica.normalmode.SimOverlapLJ
-
- basis - Variable in class etomica.normalmode.SimOverlapLJModule
-
- basis - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- basis - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- basis - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- basis - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- basis - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- basis - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- basis - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- basis - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- basis - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- basis - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- basis - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- basis - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- basis - Variable in class etomica.normalmode.SimTargetUmbrella
-
- basis - Variable in class etomica.normalmode.SimUmbrella
-
- basis - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- basis - Variable in class etomica.potential.EwaldSummation
-
- basis - Variable in class etomica.potential.P2QChemInterpolated
-
- basis - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
-
- basis - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
-
- basis - Variable in class etomica.potential.P3QChem.DampingParams
-
- BasisBetaSnA5 - Class in etomica.lattice.crystal
-
Basis that helps construct a beta-tin crystal.
- BasisBetaSnA5() - Constructor for class etomica.lattice.crystal.BasisBetaSnA5
-
- BasisBigCell - Class in etomica.normalmode
-
- BasisBigCell(Space, Basis, int[]) - Constructor for class etomica.normalmode.BasisBigCell
-
- basisCell - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- basisCell - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- BasisCell(IMoleculeList, Vector) - Constructor for class etomica.normalmode.CoordinateDefinition.BasisCell
-
- BasisCubicBcc - Class in etomica.lattice.crystal
-
A 2-atom basis for a bcc crystal
- BasisCubicBcc() - Constructor for class etomica.lattice.crystal.BasisCubicBcc
-
Makes a bcc 2-atom basis.
- BasisCubicDiamond - Class in etomica.lattice.crystal
-
An 8-atom basis that for a diamond crystal.
- BasisCubicDiamond() - Constructor for class etomica.lattice.crystal.BasisCubicDiamond
-
Makes a diamond-on-fcc 8-atom basis.
- BasisCubicFcc - Class in etomica.lattice.crystal
-
A 4-atom basis fot an fcc crystal.
- BasisCubicFcc() - Constructor for class etomica.lattice.crystal.BasisCubicFcc
-
Makes a fcc 4-atom basis.
- BasisCubicFccDiamond - Class in etomica.lattice.crystal
-
A 2-atom basis that makes a diamond crystal using a BravaisLattice
having a Cubic primitive with an fcc basis.
- BasisCubicFccDiamond() - Constructor for class etomica.lattice.crystal.BasisCubicFccDiamond
-
Makes a diamond-on-fcc 2-atom basis using the given factory to make the atoms.
- basisDim - Variable in class etomica.normalmode.NormalModesMolecular
-
- basisFCC - Variable in class etomica.normalmode.HessianDB
-
- BasisHcp - Class in etomica.lattice.crystal
-
A 2-atom basis for an hcp crystal.
- BasisHcp() - Constructor for class etomica.lattice.crystal.BasisHcp
-
- BasisHcp4 - Class in etomica.lattice.crystal
-
A 4-atom basis for an hcp crystal.
- BasisHcp4() - Constructor for class etomica.lattice.crystal.BasisHcp4
-
- BasisHcpBaseCentered - Class in etomica.lattice.crystal
-
A 2-atom basis for an hcp crystal
(base-centered or side-centered)
- BasisHcpBaseCentered() - Constructor for class etomica.lattice.crystal.BasisHcpBaseCentered
-
- basisMolecules - Variable in class etomica.modules.sam.ConfigurationSAM
-
- BasisMonatomic - Class in etomica.lattice.crystal
-
Single-atom basis with the coordinate at the origin.
- BasisMonatomic(Space) - Constructor for class etomica.lattice.crystal.BasisMonatomic
-
Creates a single-atom basis with the coordinate at the origin.
- BasisMonoclinicParacetamol - Class in etomica.paracetamol
-
An 4-atom basis that for a monoclinic paracetamol crystal.
- BasisMonoclinicParacetamol() - Constructor for class etomica.paracetamol.BasisMonoclinicParacetamol
-
Makes a monoclinic-crystal paracetamol 4-atom basis.
- basisOrientation - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- basisOrientation - Variable in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
- BasisOrthorhombicHexagonal - Class in etomica.lattice.crystal
-
A 2D hexagonal 2-atom basis
- BasisOrthorhombicHexagonal() - Constructor for class etomica.lattice.crystal.BasisOrthorhombicHexagonal
-
Makes a 2D hexagonal 2-atom basis
- BasisOrthorhombicHexagonal3D(Space) - Constructor for class etomica.modules.catalysis.ConfigurationCatalysis.BasisOrthorhombicHexagonal3D
-
Makes a fcc 4-atom basis.
- BasisOrthorhombicParacetamol - Class in etomica.paracetamol
-
An 8-atom basis that for a orthorhombic paracetamol crystal.
- BasisOrthorhombicParacetamol() - Constructor for class etomica.paracetamol.BasisOrthorhombicParacetamol
-
Makes a orthorhombic-crystal paracetamol 8-atom basis.
- basisSize() - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
Returns 2, indicating that the setBasis method expects an array of two
atoms.
- basisSize() - Method in class etomica.atom.iterator.ANIntergroupExchange
-
Returns 2, indicating that the setBasis method expects an array of two
atoms.
- basisSize() - Method in class etomica.atom.iterator.ANIntragroupExchange
-
Returns 2, indicating that the setBasis method expects an array of two
atoms.
- basisSize() - Method in class etomica.atom.iterator.ApiIndexList
-
- basisSize() - Method in class etomica.atom.iterator.ApiIntergroup
-
Returns 2, indicating that the setBasis method expects an array of two
atoms.
- basisSize() - Method in class etomica.atom.iterator.ApiIntragroup
-
Returns 1, indicating the the array given to the setBasis method
should have only one element.
- basisSize() - Method in class etomica.atom.iterator.AtomIteratorBasis
-
Returns 1, indicating that only a single-atom basis is appropriate.
- basisSize() - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart
-
Returns 1, indicating that only a single-atom basis is appropriate.
- basisSize() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
- basisSize() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
- basisSize() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
- basisSize() - Method in interface etomica.atom.iterator.AtomsetIteratorBasisDependent
-
Indicates the size of the basis needed to set the iterator.
- basisSize() - Method in class etomica.atom.iterator.TripletInnerSequential
-
- basisSize() - Method in interface etomica.molecule.iterator.MoleculesetIteratorBasisDependent
-
Indicates the size of the basis needed to set the iterator.
- basisSize() - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- basisSurface - Variable in class etomica.modules.sam.ConfigurationSAM
-
- bB - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- bB - Static variable in class etomica.potential.P2NitrogenHellmann
-
- BBbonded - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- bbcageTickEdges - Static variable in class org.jmol.util.BoxInfo
-
- bBond - Variable in class etomica.virial.cluster.VirialDiagrams
-
- bBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- bCalc(int) - Method in class etomica.veos.QSeries
-
Computes the coefficient b_j based on the beta coefficients given by the BetaSource.
- BCC - Static variable in class etomica.normalmode.SoftSphereSolidEOS
-
- BCC - Static variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- BCVisitor - Class in etomica.graph.traversal
-
This TraversalVisitor visits nodes and keeps track of biconnected
components.
- BCVisitor(List<List<Byte>>) - Constructor for class etomica.graph.traversal.BCVisitor
-
- BDbeta - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- BDlog(BigDecimal) - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- BDONE - Static variable in class etomica.virial.ClusterWheatleySoftBD
-
- BDONE - Static variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- BDONE - Static variable in class etomica.virial.MeterVirialBDBin
-
- bdrij - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- bdrij - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- bdry - Variable in class etomica.models.hexane.HexaneVolumeFraction
-
- bdry - Variable in class etomica.models.hexane.SimHarmonicHexane
-
- bdry - Variable in class etomica.models.hexane.TestHexane
-
- bdry - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
-
- bdry - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- bdry - Variable in class etomica.models.hexane.TestHexaneHarmonic
-
- bdry - Variable in class etomica.models.hexane.TestSetToUHexane
-
- bdry - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- bdry - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- bdry - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
-
- bdry - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
-
- bdry - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
-
- bdry - Variable in class etomica.models.oneDHardRods.SimWidomMode
-
- bdry - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- bdry - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- bdry - Variable in class etomica.normalmode.SimCalcJ
-
- bdry - Variable in class etomica.normalmode.SimCalcS
-
- bdry - Variable in class etomica.normalmode.SimModesJ
-
- bdry - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- bdry - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- bdry - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- bdry - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- bdry - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
-
- bdry - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
-
- bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- bdryRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- bdryTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- BDZERO - Static variable in class etomica.virial.ClusterWheatleySoftBD
-
- BDZERO - Static variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- BDZERO - Static variable in class etomica.virial.MeterVirialBD
-
- BDZERO - Static variable in class etomica.virial.MeterVirialBDBin
-
- BDZERO - Static variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- BDZERO - Static variable in class etomica.virial.MeterVirialSWWE
-
- beadFac - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- beadFac - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- beadFac - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- beadFac - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- beadFac - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- beginRendering(Matrix3f) - Method in class org.jmol.g3d.Graphics3D
-
- beginRendering(Matrix3f) - Method in class org.jmol.util.GData
-
- benBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- benBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- BenchSimDCVGCMD - Class in etomica.simulation
-
- BenchSimDCVGCMD() - Constructor for class etomica.simulation.BenchSimDCVGCMD
-
- BenchSimHSMD3D - Class in etomica.simulation
-
- BenchSimHSMD3D() - Constructor for class etomica.simulation.BenchSimHSMD3D
-
- BenchSimLJGCMC3D - Class in etomica.simulation
-
- BenchSimLJGCMC3D() - Constructor for class etomica.simulation.BenchSimLJGCMC3D
-
- BenchSimLJMC3D - Class in etomica.simulation
-
- BenchSimLJMC3D() - Constructor for class etomica.simulation.BenchSimLJMC3D
-
- BenchSimSurfacetensionLJMC - Class in etomica.simulation
-
- BenchSimSurfacetensionLJMC() - Constructor for class etomica.simulation.BenchSimSurfacetensionLJMC
-
- BenchSimSWChain - Class in etomica.simulation
-
- BenchSimSWChain() - Constructor for class etomica.simulation.BenchSimSWChain
-
- BenchVector3D - Class in etomica.space
-
- BenchVector3D() - Constructor for class etomica.space.BenchVector3D
-
- bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- bennettNumSteps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- bennetUDiff - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- Bernoulli - Class in etomica.veos.bigdecimal
-
Bernoulli numbers.
- Bernoulli() - Constructor for class etomica.veos.bigdecimal.Bernoulli
-
- besselI(double, double) - Static method in class etomica.math.SpecialFunctions
-
The modified Bessel function of the first kind, I
Reference: http://mathworld.wolfram.com/ModifiedBesselFunctionoftheFirstKind.html
- besselJ(double, double) - Static method in class etomica.math.SpecialFunctions
-
The unmodified Bessel function of the first kind, J.
- beta - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- beta - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- beta - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- beta - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- beta - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
-
- beta - Variable in class etomica.models.hexane.MCMoveCBMC
-
- beta - Variable in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
-
- beta - Static variable in class etomica.potential.P1HydrogenMielke
-
- beta - Variable in class etomica.potential.P4TorsionDreiding
-
- beta(int) - Method in interface etomica.veos.BetaSource
-
- beta(int) - Method in class etomica.veos.HardRods
-
- beta(int) - Method in class etomica.veos.VanderWaals
-
- beta - Variable in class etomica.virial.ClusterChainSoft
-
- beta - Variable in class etomica.virial.ClusterExchange
-
- beta - Variable in class etomica.virial.ClusterSinglyConnected
-
- beta - Variable in class etomica.virial.ClusterSum
-
- beta - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- beta - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- beta - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- beta - Variable in class etomica.virial.ClusterTree
-
- beta - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- beta - Variable in class etomica.virial.ClusterWheatleyHS
-
- beta - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- beta - Variable in class etomica.virial.ClusterWheatleySoft
-
- beta - Variable in class etomica.virial.ClusterWheatleySoftBD
-
- beta - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- beta - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- beta3 - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta3 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- beta3_111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta3_111 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- beta3_112 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta3_113 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta3_122 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta3_222 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta4211 - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta4211 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- beta4211 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- beta4211_1112 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta4211_1121 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta4211_2111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta4220 - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta4220 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- beta4220 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- beta4220_1111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta4220_1211 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- beta4220_2111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- betaCoeffs - Variable in class etomica.models.nitrogen.FindTransitionTemperature
-
- BetaPhaseLatticeParameter - Class in etomica.models.nitrogen
-
The parameters that are determined through conjugate gradient method to give the lowest lattice energy
for beta-N2 phase structure
- BetaPhaseLatticeParameter() - Constructor for class etomica.models.nitrogen.BetaPhaseLatticeParameter
-
- BetaPhaseLatticeParameterLS - Class in etomica.models.nitrogen
-
The parameters that are determined through conjugate gradient method to give the lowest lattice energy
for beta-N2 phase structure
for lattice sum, rC = 250 A
- BetaPhaseLatticeParameterLS() - Constructor for class etomica.models.nitrogen.BetaPhaseLatticeParameterLS
-
- BetaPhaseLatticeParameterNA - Class in etomica.models.nitrogen
-
The parameters that are determined through conjugate gradient method to give the lowest lattice energy
for beta-N2 phase structure
- BetaPhaseLatticeParameterNA() - Constructor for class etomica.models.nitrogen.BetaPhaseLatticeParameterNA
-
- BetaSource - Interface in etomica.veos
-
- betaUAB - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- betaUAB - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- betaUAW - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- betaUAW - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- betaUAWf - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- betaUAWf - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- betaUBA - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- betaUBA - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- betaUBW - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- betaUBW - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- betaUBWf - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- betaUBWf - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- bgcolor - Variable in class org.jmol.util.GData
-
- bGuess - Variable in class etomica.math.numerical.VirialOptimizer
-
- BHS(int, double) - Static method in class etomica.virial.cluster.Standard
-
Returns the nth virial coefficient for hard spheres of diameter sigma.
- BIAS - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- BIAS - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- bias - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- bias - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- biasInsert(IAtom, IAtom) - Method in class etomica.association.BiasVolume
-
- biasInsert(IMolecule, IMolecule) - Method in class etomica.association.BiasVolumeAceticAcid
-
- biasInsert(IAtom, IAtom) - Method in class etomica.association.BiasVolumeCube
-
- biasInsert(IMolecule, IMolecule) - Method in class etomica.association.BiasVolumeMolecule
-
- biasInsert(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphere
-
- biasInsert(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphereOriented
-
- biasInsert(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
- biasOld - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- BiasVolume - Class in etomica.association
-
- BiasVolume(Space) - Constructor for class etomica.association.BiasVolume
-
- biasVolume() - Method in class etomica.association.BiasVolume
-
- biasVolume() - Method in class etomica.association.BiasVolumeAceticAcid
-
- biasVolume() - Method in class etomica.association.BiasVolumeCube
-
- biasVolume() - Method in class etomica.association.BiasVolumeMolecule
-
- biasVolume() - Method in class etomica.association.BiasVolumeSphere
-
- biasVolume() - Method in class etomica.association.BiasVolumeSphereOriented
-
- biasVolume() - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
- BiasVolume2SiteAceticAcid - Class in etomica.association
-
- BiasVolume2SiteAceticAcid(Space, IRandom) - Constructor for class etomica.association.BiasVolume2SiteAceticAcid
-
- BiasVolumeAceticAcid - Class in etomica.association
-
- BiasVolumeAceticAcid(Space, IRandom, Box) - Constructor for class etomica.association.BiasVolumeAceticAcid
-
- BiasVolumeCube - Class in etomica.association
-
- BiasVolumeCube(Space, IRandom) - Constructor for class etomica.association.BiasVolumeCube
-
- BiasVolumeMolecule - Class in etomica.association
-
- BiasVolumeMolecule(Space) - Constructor for class etomica.association.BiasVolumeMolecule
-
- BiasVolumeSphere - Class in etomica.association
-
- BiasVolumeSphere(Space, IRandom) - Constructor for class etomica.association.BiasVolumeSphere
-
- BiasVolumeSphereOriented - Class in etomica.association
-
- BiasVolumeSphereOriented(Space, IRandom) - Constructor for class etomica.association.BiasVolumeSphereOriented
-
- BiasVolumeSphereOrientedDoubleSites - Class in etomica.association
-
- BiasVolumeSphereOrientedDoubleSites(Space, IRandom) - Constructor for class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
- BiComponentSubst - Class in etomica.graph.operations
-
This class handles the substitution g = A where g is a Graph and A is a set
of Graph.
- BiComponentSubst() - Constructor for class etomica.graph.operations.BiComponentSubst
-
- BiComponentSubst.BiComponentSubstParameters - Class in etomica.graph.operations
-
- BiComponentSubstParameters(Graph, Set<Graph>, boolean, boolean) - Constructor for class etomica.graph.operations.BiComponentSubst.BiComponentSubstParameters
-
- BiconectedNodalPoint - Class in etomica.graph.traversal
-
- BiconectedNodalPoint() - Constructor for class etomica.graph.traversal.BiconectedNodalPoint
-
- Biconnected - Class in etomica.graph.traversal
-
- Biconnected() - Constructor for class etomica.graph.traversal.Biconnected
-
- bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- bigAngle - Static variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- BigComplex - Class in etomica.veos.bigdecimal
-
Complex numbers with BigDecimal real and imaginary components
- BigComplex() - Constructor for class etomica.veos.bigdecimal.BigComplex
-
Default ctor equivalent to zero.
- BigComplex(BigDecimal, BigDecimal) - Constructor for class etomica.veos.bigdecimal.BigComplex
-
ctor with real and imaginary parts
- BigComplex(BigDecimal) - Constructor for class etomica.veos.bigdecimal.BigComplex
-
ctor with real part.
- BigComplex(double, double) - Constructor for class etomica.veos.bigdecimal.BigComplex
-
ctor with real and imaginary parts
- BigDecimalMath - Class in etomica.veos.bigdecimal
-
BigDecimal special functions.
- BigDecimalMath() - Constructor for class etomica.veos.bigdecimal.BigDecimalMath
-
- BigDecimalValue(MathContext) - Method in class etomica.veos.bigdecimal.BigSurd
-
Return the approximate floating point representation.
- BigDecimalValue(MathContext) - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Construct an approximate floating point representation
- BigDecimalValue(MathContext) - Method in class etomica.veos.bigdecimal.Rational
-
Return a representation as BigDecimal.
- BigIntegerMath - Class in etomica.veos.bigdecimal
-
BigInteger special functions and Number theory.
- BigIntegerMath() - Constructor for class etomica.veos.bigdecimal.BigIntegerMath
-
- BigIntegerPoly - Class in etomica.veos.bigdecimal
-
Polynomial with integer coefficients.
- BigIntegerPoly() - Constructor for class etomica.veos.bigdecimal.BigIntegerPoly
-
Default ctor.
- BigIntegerPoly(String) - Constructor for class etomica.veos.bigdecimal.BigIntegerPoly
-
Ctor with a comma-separated list as the list of coefficients.
- BigIntegerPoly(Vector<BigInteger>) - Constructor for class etomica.veos.bigdecimal.BigIntegerPoly
-
Ctor with a list of coefficients.
- BigIntegerPoly(BigInteger[]) - Constructor for class etomica.veos.bigdecimal.BigIntegerPoly
-
Ctor with a list of coefficients.
- bigomega() - Method in class etomica.veos.bigdecimal.Ifactor
-
The sum of the prime factor exponents, with multiplicity.
- BigSurd - Class in etomica.veos.bigdecimal
-
Square roots on the real line.
- BigSurd() - Constructor for class etomica.veos.bigdecimal.BigSurd
-
Default ctor, which represents the zero.
- BigSurd(Rational, Rational) - Constructor for class etomica.veos.bigdecimal.BigSurd
-
ctor given the prefactor and the basis of the root.
- BigSurd(int, int) - Constructor for class etomica.veos.bigdecimal.BigSurd
-
ctor given the numerator and denominator of the root.
- BigSurd(BigInteger) - Constructor for class etomica.veos.bigdecimal.BigSurd
-
ctor given the value under the root.
- BigSurdVec - Class in etomica.veos.bigdecimal
-
A BigSurdVec represents an algebraic sum or differences of values
which each term an instance of BigSurd.
- BigSurdVec() - Constructor for class etomica.veos.bigdecimal.BigSurdVec
-
Default ctor, which represents the zero.
- BigSurdVec(BigSurd) - Constructor for class etomica.veos.bigdecimal.BigSurdVec
-
ctor given the value of a BigSurd.
- BigSurdVec(BigSurd, BigSurd) - Constructor for class etomica.veos.bigdecimal.BigSurdVec
-
ctor given two values, which (when added) represent this number a+b.
- BigValue - Class in etomica.veos
-
Data class to handle operations involving large numbers.
- BigValue() - Constructor for class etomica.veos.BigValue
-
Default constructor sets value to 0.0
- BigValue(double) - Constructor for class etomica.veos.BigValue
-
Constructs using the given value.
- BigValue(double, boolean) - Constructor for class etomica.veos.BigValue
-
Constructs given ln(|value|) and sign of value.
- BigValue(IBigValue) - Constructor for class etomica.veos.BigValue
-
Copy constructor.
- Binary - Interface in etomica.graph.operations
-
- BINARY_OP_CONV - Static variable in interface etomica.graph.engine.Parser
-
- BINARY_OP_DEL - Static variable in interface etomica.graph.engine.Parser
-
- BINARY_OP_MUL - Static variable in interface etomica.graph.engine.Parser
-
- BINARY_OP_SUB - Static variable in interface etomica.graph.engine.Parser
-
- BINARY_OP_SUM - Static variable in interface etomica.graph.engine.Parser
-
- BINARY_OP_UNION - Static variable in interface etomica.graph.engine.Parser
-
- binaryExtensions - Static variable in class org.jmol.viewer.JmolConstants
-
- BinaryOpByteImpl - Class in etomica.graph.engine.impl
-
- BinaryOpByteImpl(String, Parser.Expression, Parser.Expression, byte) - Constructor for class etomica.graph.engine.impl.BinaryOpByteImpl
-
- BinaryOpImpl - Class in etomica.graph.engine.impl
-
- BinaryOpImpl(String, Parser.Expression, Parser.Expression) - Constructor for class etomica.graph.engine.impl.BinaryOpImpl
-
- binom - Static variable in class etomica.potential.P2O2Bartolomei
-
- binomial(int, int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate binomial(n,k).
- binomial(BigInteger, BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate binomial(n,k).
- binomial(Rational, BigInteger) - Static method in class etomica.veos.bigdecimal.Rational
-
binomial (n choose m).
- binomial(Rational, int) - Static method in class etomica.veos.bigdecimal.Rational
-
binomial (n choose m).
- binomial - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- binomial - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- binomialTInv(int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Inverse Binomial transform.
- binSize - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- binSize - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- binSize - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- bisectorVec - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- BishopPipin(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
-
- BishopPipin(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- bitCount() - Method in interface etomica.graph.model.Bitmap
-
Returns the number of bits set in the bitmap.
- bitCount() - Method in class etomica.graph.model.impl.AbstractBitmap
-
- bitCount(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
Returns the number of valid bits in the long with the given index.
- Bitmap - Interface in etomica.graph.model
-
Abstracts away the form in which bitmaps implement their operations and store their
data.
- BitmapFactory - Class in etomica.graph.model
-
- BitmapFactory() - Constructor for class etomica.graph.model.BitmapFactory
-
- BitmapOfLong - Class in etomica.graph.model.impl
-
This class encodes edges in a space efficient fashion, with the limitation that it can
only encode up to 64 bits.
- BitmapOfLong(Bitmap) - Constructor for class etomica.graph.model.impl.BitmapOfLong
-
- BitmapOfLong(int) - Constructor for class etomica.graph.model.impl.BitmapOfLong
-
- BitmapOfLong(int, boolean) - Constructor for class etomica.graph.model.impl.BitmapOfLong
-
- BitmapOfLong(String) - Constructor for class etomica.graph.model.impl.BitmapOfLong
-
- BitmapOfLong(byte[]) - Constructor for class etomica.graph.model.impl.BitmapOfLong
-
- BitmapOfLong() - Constructor for class etomica.graph.model.impl.BitmapOfLong
-
- BitmapOfLongVector - Class in etomica.graph.model.impl
-
Transparent implementation of arbitrarily large bitmaps based on an array of long
values.
- BitmapOfLongVector(Bitmap) - Constructor for class etomica.graph.model.impl.BitmapOfLongVector
-
- BitmapOfLongVector(int) - Constructor for class etomica.graph.model.impl.BitmapOfLongVector
-
- BitmapOfLongVector(int, boolean) - Constructor for class etomica.graph.model.impl.BitmapOfLongVector
-
- BitmapOfLongVector(String) - Constructor for class etomica.graph.model.impl.BitmapOfLongVector
-
- BitmapOfLongVector(byte[]) - Constructor for class etomica.graph.model.impl.BitmapOfLongVector
-
- BitmapUtils - Class in etomica.graph.traversal
-
- BitmapUtils() - Constructor for class etomica.graph.traversal.BitmapUtils
-
- bitMask(byte) - Static method in class etomica.graph.traversal.BitmapUtils
-
- bitOffMask(byte) - Static method in class etomica.graph.traversal.BitmapUtils
-
- bitOffset(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
The highest order bit is at bit 0 of bitmap[0], and the lowest order bit is at bit
bitSize() - 1 of bitmap[size()-1].
- bitOnMask(byte) - Static method in class etomica.graph.traversal.BitmapUtils
-
- bitset - Static variable in class org.jmol.script.Token
-
- BitSet - Class in org.jmol.util
-
a fast 64-bit BitSet optimized for Java2Script -- about 25 times faster than
java.util.BitSet in JavaScript
- BitSet() - Constructor for class org.jmol.util.BitSet
-
Creates a new bit set.
- BitSetUtil - Class in org.jmol.util
-
- BitSetUtil() - Constructor for class org.jmol.util.BitSetUtil
-
- bitSize() - Method in interface etomica.graph.model.Bitmap
-
Returns the length in bits of the bitmap.
- bitSize() - Method in class etomica.graph.model.impl.BitmapOfLong
-
- bitSize() - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- bl - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- BLACK - Static variable in class org.jmol.util.Colix
-
- blankPanel - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- blMax - Static variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- blN2 - Static variable in class etomica.potential.P2NitrogenHellmann
-
- blN2 - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- blN2 - Static variable in class etomica.virial.simulations.VirialN2
-
- blN2 - Static variable in class etomica.virial.simulations.VirialN2PI
-
- blO2 - Static variable in class etomica.virial.simulations.VirialO2PI
-
- BLOCK_CORRELATION - Static variable in class etomica.data.AccumulatorAverage
-
- BLOCK_COVARIANCE - Static variable in class etomica.data.AccumulatorAverageCovariance
-
- blockAccumulator - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- blockCorrelation - Variable in class etomica.data.AccumulatorAverage
-
- blockCountDown - Variable in class etomica.data.AccumulatorAverage
-
- blockCounter - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- blockCounter - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- blockCounter - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- blockCovariance - Variable in class etomica.data.AccumulatorAverageCovariance
-
- blockCovSum - Variable in class etomica.data.AccumulatorAverageCovariance
-
- blockDataSink - Variable in class etomica.data.AccumulatorAverageFixed
-
- blocks - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- blocks - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- blocks - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- blocks - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- blocksEq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- blocksEq - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- blocksEq - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- blocksEq - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- blockSize - Variable in class etomica.data.AccumulatorAverage
-
- blockSize - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- blockSize - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- blockSize - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- blockSize - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- blockSize - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
-
- blockSize - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- blockSize - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
-
- blockSize - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- blockSize - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- blockSize - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- blockSize - Variable in class etomica.virial.simulations.VirialLJD.VirialLJParam
-
- blockSums - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- blockSums - Variable in class etomica.data.AccumulatorAverageCollapsing
-
- blockSums - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- blOption - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- blOption - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- BLUE - Static variable in class org.jmol.util.Colix
-
- bmu - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- bmu - Variable in class etomica.normalmode.DataSourceAvgPressure
-
- bmu - Variable in class etomica.normalmode.DataSourceAvgPressure2
-
- bmu - Variable in class etomica.normalmode.DataSourceFEHistogram
-
- bmu - Variable in class etomica.normalmode.DataSourceImposedFEFit
-
- bmu - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
-
- bmu - Variable in class etomica.normalmode.DataSourceMuRoot
-
- bmu - Variable in class etomica.normalmode.DataSourceMuRoot1
-
- bmu - Variable in class etomica.normalmode.DataSourceMuRootPMatch
-
- bmu - Variable in class etomica.normalmode.DataSourcePMu
-
- bmuLat - Variable in class etomica.normalmode.DataSourceMuRoot
-
- BnFlexibleContributionTraPPEUAMethanol - Class in etomica.virial.simulations
-
Computes (part of) the flexible contribution to the virial coefficient
for the TraPPE-UA model of methanol (http://www.chem.umn.edu/groups/siepmann/trappe/intro.php)
K.R.S.
- BnFlexibleContributionTraPPEUAMethanol() - Constructor for class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol
-
- BnFlexibleContributionTraPPEUAMethanol.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- BnHNCLJ - Class in etomica.virial
-
This is just a main method for HypernettedChain.java...
- BnHNCLJ() - Constructor for class etomica.virial.BnHNCLJ
-
- BnHSIonic - Class in etomica.virial
-
ionic solution, restrictive primitive model (RPM)
compute s, (phi[osmotic coefficient]-1) and ln(gamma) from HARD SPHERE interaction(from Standard class)
2nd ~ 5th order integrals are included
p[] (<==> HSB[]) ==> integral = HSB[]* n! / (1-n)
s[n] = c^n * HSB[n] / (1-n)
ds[n]/dc = n * c ^ (n-1) * HSB[n] / (1-n) = s[n] * n/c cuz integral is independent of concentration
in simulation units
contains "linear step in sqrt(c)" && "linear step in c"
- BnHSIonic() - Constructor for class etomica.virial.BnHSIonic
-
- BnIETP2Spherical - Class in etomica.virial
-
This is just a main method for HypernettedChain.java or PercusYevick.java...
- BnIETP2Spherical() - Constructor for class etomica.virial.BnIETP2Spherical
-
- BnJHBVArgon_Analytic - Class in etomica.virial
-
Computes virial coefficients for argon using the analytical expressions
developed by Jaeger, Hellmann, Bich, and Vogel (2011), JCP, 135: 084308.
- BnJHBVArgon_Analytic() - Constructor for class etomica.virial.BnJHBVArgon_Analytic
-
- BnPY_1QC_Helium - Class in etomica.virial
-
Computes the Percus-Yevick compressibility-route approximation for to the
first quantum correction of Bn, where the first quantum correction is
as defined Kim and Henderson (1968,1966).
- BnPY_1QC_Helium() - Constructor for class etomica.virial.BnPY_1QC_Helium
-
- BnPYCHe - Class in etomica.virial
-
This is just a main method for PercusYevick.java.
- BnPYCHe() - Constructor for class etomica.virial.BnPYCHe
-
- BnPYCHe.BnPYHeParams - Class in etomica.virial
-
- BnPYHardSphere - Class in etomica.virial
-
This is just a main method for PercusYevick.java...
- BnPYHardSphere() - Constructor for class etomica.virial.BnPYHardSphere
-
- BnPYHeParams() - Constructor for class etomica.virial.BnPYCHe.BnPYHeParams
-
- BnPYLJ - Class in etomica.virial
-
This is just a main method for PercusYevick.java.
- BnPYLJ() - Constructor for class etomica.virial.BnPYLJ
-
- BnSCALJ - Class in etomica.virial
-
Combines the Percus-Yevick and hypernetted-chain approximations to the virial coefficients to
generate a self-consistent (thermodynamically consistent) approximation.
- BnSCALJ() - Constructor for class etomica.virial.BnSCALJ
-
- bohrConv - Variable in class etomica.models.water.P2WaterSzalewicz
-
- BohrRadius - Class in etomica.units
-
The Borh Radius unit of length, corresponding to the size of a Hydrogen
atom's electron cloud.
- BOLTZMANN_K - Static variable in class etomica.util.Constants
-
Boltzmann's constant, in (sim units)/kelvin.
- boltzmannAverage - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
-
- boltzmannAverage - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
-
- boltzmannAverage - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
-
- boltzmannAverage - Variable in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
-
- BoltzmannProcessor - Class in etomica.normalmode
-
DataProcessor that returns the Boltzmann factor of the incoming energy.
- BoltzmannProcessor() - Constructor for class etomica.normalmode.BoltzmannProcessor
-
- bond(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
this function will bond atoms a & b together
- bond(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
this function will bond atoms a & b together
- bond - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
-
- bond - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
-
- Bond - Class in g3dsys.images
-
- Bond(G3DSys, Ball, Ball) - Constructor for class g3dsys.images.Bond
-
- Bond(G3DSys, Ball, Ball, short) - Constructor for class g3dsys.images.Bond
-
- BOND_ORDER_MAP - Static variable in interface etomica.graph.model.Metadata
-
- BONDAC - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
-
- BONDAC - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
-
- BondArrayList() - Constructor for class etomica.potential.P2HardBondedList.BondArrayList
-
- BONDBC - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
-
- BONDBC - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
-
- BONDCA - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
-
- BONDCA - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
-
- BONDCB - Static variable in class etomica.models.water.P2HardAssociationGCPMReference
-
- BONDCB - Static variable in class etomica.models.water.PNWaterGCPMThreeSite
-
- BondChangeData() - Constructor for class etomica.potential.PotentialReactive.BondChangeData
-
- BondConnectedSubstitution - Class in etomica.virial.cluster
-
If Wertheim diagrams have bond connected network, fR bond is split into eR and -one bond.
- BondConnectedSubstitution() - Constructor for class etomica.virial.cluster.BondConnectedSubstitution
-
- BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site - Class in etomica.virial.cluster
-
- BondConnectedSubstitution3Site - Class in etomica.virial.cluster
-
If Wertheim diagrams have bond connected network, fR bond is split into eR and -one bond.
- BondConnectedSubstitution3Site() - Constructor for class etomica.virial.cluster.BondConnectedSubstitution3Site
-
- BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site - Class in etomica.virial.cluster
-
- BondConnectedSubstitutionNaphthalene - Class in etomica.virial.cluster
-
revised from Hye Min's "BondConnectedSubstitution"
If Wertheim diagrams have bond connected network, fR bond is split into eR and -one bond.
- BondConnectedSubstitutionNaphthalene() - Constructor for class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene
-
- BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa - Class in etomica.virial.cluster
-
- BondConnectedSubstitutionParameters2Site(char, char) - Constructor for class etomica.virial.cluster.BondConnectedSubstitution.BondConnectedSubstitutionParameters2Site
-
- BondConnectedSubstitutionParameters2SiteNa(char, char, List<Character>, List<Character>, List<Character>, List<Character>) - Constructor for class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
-
- BondConnectedSubstitutionParameters3Site(char, char) - Constructor for class etomica.virial.cluster.BondConnectedSubstitution3Site.BondConnectedSubstitutionParameters3Site
-
- BondConstraints(int[][], double[]) - Constructor for class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
-
- bondCount - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded.RingResult
-
- bondcount - Static variable in class org.jmol.script.Token
-
- bondDecomp - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- bondDecomp - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- bondDecomp - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- bondDecomp - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- bondDecomp - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- bondedAtom1 - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
-
- bondedAtom2 - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
-
- bondedAtoms - Variable in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
-
- bondedAtoms - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- bondedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- bondedSet - Variable in class etomica.modules.render.RenderMD.CriterionCar
-
- bondFac - Variable in class etomica.modules.colloid.P2HardSphereMC
-
- bondFac - Variable in class etomica.modules.colloid.P2SquareWellMonomer
-
- bondIndexArray - Variable in class etomica.virial.ClusterBonds
-
- BondInfo(int, int, double) - Constructor for class etomica.modules.render.ParseObj.BondInfo
-
- bondingAgentManager - Variable in class etomica.modules.chainequilibrium.ColorSchemeStepWise
-
- bondingAngleRestriction - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
-
- bondingAngleRestriction - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
-
- bondingAngleRestriction - Variable in class etomica.models.water.PNWaterGCPMThreeSite
-
- bondingPotential - Variable in class etomica.chem.models.ModelChain
-
- BondInteractionTypeToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.BondInteractionTypeToggler
-
- bondIteratorsHash - Variable in class etomica.graphics.BondListener
-
- bondL - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- bondL - Variable in class etomica.virial.Conformation7SiteRigidSF6
-
- bondL - Variable in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- bondL - Variable in class etomica.virial.SpeciesFactorySpheres2
-
- bondL_CC - Variable in class etomica.modules.sam.Sam
-
- bondLength - Variable in class etomica.atom.AtomHydrogen
-
- bondLength - Variable in class etomica.config.ConformationLinear
-
- bondlength - Variable in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- bondlength - Static variable in class etomica.virial.ConformationAnthracene3site
-
- bondlength - Static variable in class etomica.virial.ConformationCO2
-
- bondlength - Static variable in class etomica.virial.ConformationNaphthaleneTraPPE
-
- bondlength - Static variable in class etomica.virial.ConformationPh3site
-
- bondLength - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- bondLength - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- bondLengthOH - Static variable in class etomica.models.water.ConformationWater3P
-
- bondLengthOH - Static variable in class etomica.models.water.ConformationWaterTIP4P
-
- bondLengths - Variable in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
-
- bondList - Variable in class etomica.association.MCMoveAtomSmer
-
- bondList - Variable in class etomica.association.MCMoveMoleculeSmer
-
- bondList - Variable in class etomica.modules.render.ParseObj
-
- bondList - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
-
- BondListener - Class in etomica.graphics
-
BondListener listens for Atoms being added to the Simulation, determines
what covalent bonds (if any) apply to the new Atom and informs a BondManager
of any new bonds.
- BondListener(Box, BondManager) - Constructor for class etomica.graphics.BondListener
-
Creates a new BondListener for the given Box, using the given
BondManager to actually create or remove bonds.
- bondManager - Variable in class etomica.graphics.BondListener
-
- BondManager - Interface in etomica.graphics
-
The BondManager is responsible for creation and disposal of bonds between
atom pairs.
- bondManager - Variable in class etomica.modules.colloid.P2HardSphereMC
-
- bondManager - Variable in class etomica.modules.colloid.P2SquareWellMonomer
-
- bondManager - Variable in class etomica.modules.sam.CriterionTether3
-
- bondMap - Variable in class etomica.graph.operations.ExcludeParameters
-
- bondMap - Variable in class etomica.modules.render.RenderMD.P2PenetrableCar
-
- bondmodeor - Static variable in class org.jmol.script.Token
-
- bondOrigN - Static variable in class etomica.models.nitrogen.ConformationNitrogen
-
- bondOrigN - Static variable in class etomica.models.nitrogen.ConformationNitrogenShellModel
-
- bondOrigP - Static variable in class etomica.models.nitrogen.ConformationNitrogenShellModel
-
- bondOrigP1 - Static variable in class etomica.models.nitrogen.ConformationNitrogen
-
- bondOrigP2 - Static variable in class etomica.models.nitrogen.ConformationNitrogen
-
- bondpicking - Static variable in class org.jmol.script.Token
-
- bondradiusmilliangstroms - Static variable in class org.jmol.script.Token
-
- bonds - Variable in class etomica.virial.MCMoveClusterAtomHSTree
-
- bonds - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
-
- bonds - Static variable in class org.jmol.script.Token
-
- bondsA - Variable in class etomica.graph.operations.CombineABSite.CombineABSiteParameters
-
- bondsB - Variable in class etomica.graph.operations.CombineABSite.CombineABSiteParameters
-
- bondsTree - Variable in class etomica.virial.ClusterTree
-
- bondTheta - Variable in class etomica.modules.sam.Sam
-
- bondTheta - Variable in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- bondTheta - Variable in class etomica.virial.SpeciesFactorySpheres2
-
- bondtolerance - Static variable in class org.jmol.script.Token
-
- bondType - Variable in class etomica.models.OPLS.P2AceticAcidTwoSite
-
- bondTypeToggler - Variable in class etomica.modules.clustergenerator.MyApplet
-
- BondTypeToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.BondTypeToggler
-
- booleanparam - Static variable in class org.jmol.script.Token
-
- bootstrap() - Method in class etomica.graph.iterators.CartesianIterator
-
- bootstrap() - Method in class etomica.graph.iterators.CartesianPermutator
-
- BOT - Static variable in class etomica.math.Gamma
-
- BOTEXP - Static variable in class etomica.math.Gamma
-
- bothSides - Variable in class etomica.modules.adsorption.MyMCMove
-
- BOTTOM - Static variable in class etomica.graphics.DisplayBox
-
- BOTTOM - Static variable in class etomica.graphics.DisplayPolytope
-
- boundaries - Variable in class etomica.modules.rosmosis.MeterFlux
-
- boundary - Variable in class etomica.association.AssociationHelperBranched
-
- boundary - Variable in class etomica.association.AssociationHelperDouble
-
- boundary - Variable in class etomica.association.AssociationHelperMolecule
-
- boundary - Variable in class etomica.data.meter.PotentialCalculationRDF
-
- boundary - Variable in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- boundary - Variable in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- boundary - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
-
- boundary - Variable in class etomica.graphics.ColorSchemeOverlap
-
- boundary - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- boundary - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- boundary - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
- boundary - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
- boundary - Variable in class etomica.meam.P2EAM
-
- boundary - Variable in class etomica.meam.PotentialCuLREP
-
- boundary - Variable in class etomica.meam.PotentialEAM
-
- boundary - Variable in class etomica.meam.PotentialEAM_LS
-
- boundary - Variable in class etomica.meam.PotentialEFS
-
- boundary - Variable in class etomica.meam.PotentialMEAM
-
- boundary - Variable in class etomica.models.co2.PNCO2GCPM
-
- boundary - Variable in class etomica.models.co2.PNGCPM
-
- boundary - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- boundary - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- boundary - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- boundary - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- boundary - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- boundary - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- boundary - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- boundary - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
-
- boundary - Variable in class etomica.models.water.P2Water3P
-
- boundary - Variable in class etomica.models.water.P2Water4P
-
- boundary - Variable in class etomica.models.water.P2WaterTIP4PHardCore
-
- boundary - Variable in class etomica.models.water.PNWaterGCPM
-
- boundary - Variable in class etomica.models.water.TestEwaldTIP4PWater
-
- boundary - Variable in class etomica.modules.adsorption.P1Wall
-
- boundary - Variable in class etomica.modules.colloid.P1Wall
-
- boundary - Variable in class etomica.modules.interfacial.MeterOrientation
-
- boundary - Variable in class etomica.molecule.MoleculePositionGeometricCenterPBC
-
- boundary - Variable in class etomica.nbr.CriterionSimple
-
- boundary - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- boundary - Variable in class etomica.normalmode.HessianDB
-
- boundary - Variable in class etomica.normalmode.LJVacancyMin
-
- boundary - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- boundary - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- boundary - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- boundary - Variable in class etomica.normalmode.NormalModes1DHR
-
- boundary - Variable in class etomica.normalmode.NormalModes2D
-
- boundary - Variable in class etomica.normalmode.P1ConstraintNbr
-
- boundary - Variable in class etomica.normalmode.P1ConstraintNbrHcp
-
- boundary - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- boundary - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- boundary - Variable in class etomica.normalmode.SimBennet
-
- boundary - Variable in class etomica.normalmode.SimCalcSLJ
-
- boundary - Variable in class etomica.normalmode.SimCalcSMorse
-
- boundary - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
-
- boundary - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- boundary - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- boundary - Variable in class etomica.normalmode.SimEinStep1
-
- boundary - Variable in class etomica.normalmode.SimEinStep1HCP
-
- boundary - Variable in class etomica.normalmode.SimEinStep2
-
- boundary - Variable in class etomica.normalmode.SimEinStep2HCP
-
- boundary - Variable in class etomica.normalmode.SimHarmonic
-
- boundary - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- boundary - Variable in class etomica.normalmode.SimLJHTTISuper
-
- boundary - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- boundary - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- boundary - Variable in class etomica.normalmode.SimTarget
-
- boundary - Variable in class etomica.normalmode.SimTargetUmbrella
-
- boundary - Variable in class etomica.normalmode.SimUmbrella
-
- boundary - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- boundary - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
-
- boundary - Variable in class etomica.potential.P1HardBoundary
-
- boundary - Variable in class etomica.potential.P1HydrogenMielke
-
- boundary - Variable in class etomica.potential.P2CO2EMP
-
- boundary - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
-
- boundary - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
-
- boundary - Variable in class etomica.potential.P2HydrogenHinde
-
- boundary - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- boundary - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- boundary - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- boundary - Variable in class etomica.potential.P2HydrogenPatkowski
-
- boundary - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- boundary - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- boundary - Variable in class etomica.potential.P2MoleculeTruncated
-
- boundary - Variable in class etomica.potential.P2NitrogenHellmann
-
- boundary - Variable in class etomica.potential.P2O2Bartolomei
-
- boundary - Variable in class etomica.potential.P2QChem
-
- boundary - Variable in class etomica.potential.P2ReactionFieldDipole
-
- boundary - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- boundary - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- boundary - Variable in class etomica.potential.P2SoftTruncated
-
- boundary - Variable in class etomica.potential.P2SpheroPolyhedron
-
- boundary - Variable in class etomica.potential.P2WaterPotentialsJankowski
-
- boundary - Variable in class etomica.potential.P3AxilrodTeller
-
- boundary - Variable in class etomica.potential.P3BondAngle
-
- boundary - Variable in class etomica.potential.P3BondAngleDreiding
-
- boundary - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- boundary - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- boundary - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- boundary - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- boundary - Variable in class etomica.potential.P3HydrogenATM
-
- boundary - Variable in class etomica.potential.P3HydrogenManzhos
-
- boundary - Variable in class etomica.potential.P3Induction
-
- boundary - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- boundary - Variable in class etomica.potential.P4BondTorsion
-
- boundary - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- boundary - Variable in class etomica.potential.P4TorsionDreiding
-
- boundary - Variable in class etomica.potential.Potential1
-
- boundary - Variable in class etomica.potential.Potential2HardSpherical
-
- boundary - Variable in class etomica.potential.Potential2SoftSpherical
-
- boundary - Variable in class etomica.potential.Potential2SoftSphericalLS
-
- boundary - Variable in class etomica.potential.PotentialEmul
-
- Boundary - Class in etomica.space
-
Parent class of boundary objects that describe the size and periodic nature
of the box boundaries.
- Boundary(Space, Polytope) - Constructor for class etomica.space.Boundary
-
Subclasses must invoke this constructor and provide a Space instance that
can be used to generate Vectors, and a Polytope that defines the shape
and volume of the boundary region.
- boundary - Variable in class etomica.space.BoundaryEvent
-
- boundary - Variable in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
-
- boundaryCoefficients - Variable in class etomica.modules.rosmosis.MeterFlux
-
- BoundaryDeformableLattice - Class in etomica.space
-
Deformable boundary that takes the shape of a primitive with some number
of cells in each dimension.
- BoundaryDeformableLattice(Primitive, int[]) - Constructor for class etomica.space.BoundaryDeformableLattice
-
Creates boundary with the shape of the given primitive and the given
number of cells for each dimension.
- BoundaryDeformableLattice(Primitive, double[]) - Constructor for class etomica.space.BoundaryDeformableLattice
-
Creates boundary with the shape of the given primitive and the given
number of cells for each dimension.
- BoundaryDeformablePeriodic - Class in etomica.space
-
Boundary shaped as an arbitrary parallelepiped.
- BoundaryDeformablePeriodic(Space) - Constructor for class etomica.space.BoundaryDeformablePeriodic
-
Make a cubic boundary with edges of length equal to the default boxSize and
periodic in every direction.
- BoundaryDeformablePeriodic(Space, double) - Constructor for class etomica.space.BoundaryDeformablePeriodic
-
Make a cubic boundary of specified edge length and periodicity.
- BoundaryDeformablePeriodic(Space, Vector[]) - Constructor for class etomica.space.BoundaryDeformablePeriodic
-
Make a parallelepiped boundary of specified shape and periodicity.
- BoundaryDeformablePeriodicSwitch - Class in etomica.models.nitrogen
-
- BoundaryDeformablePeriodicSwitch(Space, Vector[]) - Constructor for class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
-
- BoundaryEvent - Class in etomica.space
-
Event that informs a listener about some change to a boundary.
- BoundaryEvent(Boundary) - Constructor for class etomica.space.BoundaryEvent
-
- BoundaryEventListener - Interface in etomica.space
-
Listener for boundary events.
- BoundaryEventManager - Class in etomica.space
-
Manager of listeners for boundary events.
- BoundaryEventManager() - Constructor for class etomica.space.BoundaryEventManager
-
- boundaryHardA - Variable in class etomica.modules.osmosis.OsmosisSim
-
- boundaryHardB - Variable in class etomica.modules.osmosis.OsmosisSim
-
- boundaryHarmonic - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- boundaryHarmonic - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- boundaryHarmonic - Variable in class etomica.normalmode.SimOverlap
-
- boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapLJ
-
- boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapLJModule
-
- boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- boundaryHarmonic - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- boundaryInflate(BoundaryEvent) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- boundaryInflate(BoundaryEvent) - Method in class etomica.nbr.cell.NeighborCellManager
-
- boundaryInflate(BoundaryEvent) - Method in interface etomica.space.BoundaryEventListener
-
Informs the listener that the boundary shape and/or size has changed.
- boundaryPadding - Variable in class etomica.config.ConfigurationLattice
-
- BoundaryPistonCylinder - Class in etomica.modules.pistoncylinder
-
Boundary class for PistonCylinder that accounts for the piston and collision
radius when calculating the (available) volume
- BoundaryPistonCylinder(Space) - Constructor for class etomica.modules.pistoncylinder.BoundaryPistonCylinder
-
- BoundaryRectangular - Class in etomica.space
-
Boundary that is in the shape of a rectangular parallelepiped.
- BoundaryRectangular(Space) - Constructor for class etomica.space.BoundaryRectangular
-
Constructs cubic boundary of the given periodicity, using the space and default box-size
given by the Simulation.
- BoundaryRectangular(Space, double) - Constructor for class etomica.space.BoundaryRectangular
-
Constructs cubic boundary of the given periodicity with each edge of length boxSize
- BoundaryRectangular(Space, double[]) - Constructor for class etomica.space.BoundaryRectangular
-
Constructs rectangular boundary of the given periodicity with edges given by the
values in the array boxSize.
- BoundaryRectangularNonperiodic - Class in etomica.space
-
Boundary that is not periodic in any direction.
- BoundaryRectangularNonperiodic(Space) - Constructor for class etomica.space.BoundaryRectangularNonperiodic
-
Make a boundary with unit volume.
- BoundaryRectangularPeriodic - Class in etomica.space
-
Rectangular boundary that is periodic in every dimension.
- BoundaryRectangularPeriodic(Space) - Constructor for class etomica.space.BoundaryRectangularPeriodic
-
Constructs cubic boundary with the default box-size given by the Simulation.
- BoundaryRectangularPeriodic(Space, double) - Constructor for class etomica.space.BoundaryRectangularPeriodic
-
Constructs cubic boundary for the given Space, with each edge of length boxSize.
- BoundaryRectangularPeriodic(Space, double[]) - Constructor for class etomica.space.BoundaryRectangularPeriodic
-
Constructs rectangular boundary for the given Space, with each edge of length boxSize.
- BoundaryRectangularPeriodicSwitch - Class in etomica.models.nitrogen
-
- BoundaryRectangularPeriodicSwitch(Space) - Constructor for class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
-
- BoundaryRectangularPore - Class in etomica.space
-
Class for implementing pore periodic boundary conditions, in which
one dimension is periodic.
- BoundaryRectangularPore(Space) - Constructor for class etomica.space.BoundaryRectangularPore
-
Makes cubic volume with the x-dimension (index 0)
not periodic.
- BoundaryRectangularPore(Space, int) - Constructor for class etomica.space.BoundaryRectangularPore
-
Makes cubic volume with the indicated dimension not periodic.
- BoundaryRectangularPore(Space, int, double) - Constructor for class etomica.space.BoundaryRectangularPore
-
Constructor for periodic boundary conditions with a pore
in the given dimension.
- BoundaryRectangularSlit - Class in etomica.space
-
Class for implementing slit periodic boundary conditions, in which
one dimension is not periodic.
- BoundaryRectangularSlit(Space) - Constructor for class etomica.space.BoundaryRectangularSlit
-
Makes cubic volume with the x-dimension (index 0)
not periodic.
- BoundaryRectangularSlit(int, Space) - Constructor for class etomica.space.BoundaryRectangularSlit
-
Makes cubic volume with the indicated dimension not periodic.
- BoundaryRectangularSlit(int, double, Space) - Constructor for class etomica.space.BoundaryRectangularSlit
-
Constructor for periodic boundary conditions with a slit
in the given dimension.
- boundaryRef - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- boundaryRef - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- boundaryRef - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- boundaryRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- boundarySemiB - Variable in class etomica.modules.osmosis.OsmosisSim
-
- boundaryTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- boundaryTarget - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- boundaryTarget - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- boundaryTarget - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- boundaryTarget - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- boundaryTarget - Variable in class etomica.normalmode.SimOverlap
-
- boundaryTarget - Variable in class etomica.normalmode.SimOverlapLJ
-
- boundaryTarget - Variable in class etomica.normalmode.SimOverlapLJModule
-
- boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- boundaryTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- boundaryTarget - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- BoundaryTruncatedOctahedron - Class in etomica.space3d
-
This class enables creation of a periodic truncated-octahedron boundary.
- BoundaryTruncatedOctahedron(Space) - Constructor for class etomica.space3d.BoundaryTruncatedOctahedron
-
- BoundaryTruncatedOctahedron(Space, double) - Constructor for class etomica.space3d.BoundaryTruncatedOctahedron
-
- boundbox - Static variable in class org.jmol.script.Token
-
- boundboxcolor - Static variable in class org.jmol.script.Token
-
- box - Variable in class etomica.action.ActionMinimizeEnergy
-
- box - Variable in class etomica.action.BoxActionAdapter
-
- box - Variable in class etomica.action.BoxRandomizeMomenta
-
- box - Variable in class etomica.action.BoxScaleMomenta
-
- box - Variable in class etomica.action.WriteConfiguration
-
- box - Variable in class etomica.AlkaneEH.CH4NVT
-
- box - Variable in class etomica.AlkaneEH.DHS_NVT
-
- box - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
-
- box - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- box - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- box - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- box - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- box - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- box - Variable in class etomica.atom.AtomLeafAgentManager
-
- box - Variable in class etomica.atom.AtomSourceRandomSpecies
-
- Box - Class in etomica.box
-
A Box collects all atoms that interact with one another; atoms in different
boxes do not interact.
- Box(Space) - Constructor for class etomica.box.Box
-
Constructs box with default rectangular periodic boundary.
- Box(Boundary, Space) - Constructor for class etomica.box.Box
-
Constructs box with the given Boundary, which specifies the size and shape of the Box and specifies what
happens to atoms as they cross the box boundary e.g.
- box - Variable in class etomica.box.BoxEvent
-
- box - Variable in class etomica.box.RandomPositionSourceDeformable
-
- box - Variable in class etomica.box.RandomPositionSourceRectangular
-
- box - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
-
- box - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- box - Variable in class etomica.data.DataProcessorInterfacialTension
-
- box - Variable in class etomica.data.meter.MeterDihedralAngle
-
- box - Variable in class etomica.data.meter.MeterHyperVirial
-
- box - Variable in class etomica.data.meter.MeterKineticEnergyRigid
-
- box - Variable in class etomica.data.meter.MeterPotentialEnergy
-
- box - Variable in class etomica.data.meter.MeterPressure
-
- box - Variable in class etomica.data.meter.MeterPressureTensor
-
- box - Variable in class etomica.data.meter.MeterProfileByAtoms
-
- box - Variable in class etomica.data.meter.MeterProfileByVolume
-
- box - Variable in class etomica.data.meter.MeterRDF
-
- box - Variable in class etomica.data.meter.MeterRDFPC
-
- box - Variable in class etomica.data.meter.MeterRMSD
-
- box - Variable in class etomica.data.meter.MeterStructureFactor
-
- box - Variable in class etomica.data.meter.MeterTemperature
-
- box - Variable in class etomica.data.meter.MeterWidomInsertion
-
- box - Variable in class etomica.densityofstate.DensityOfState
-
- box - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
-
- box - Variable in class etomica.dielectric.DHS_NVT
-
- box - Variable in class etomica.dielectric.DLJ_NVT_1site
-
- box - Variable in class etomica.dielectric.TIP4P_NVT
-
- box - Variable in class etomica.dimer.EnergyMap
-
- box - Variable in class etomica.dimer.PotentialCalculationForcePressureSumGB
-
- box - Variable in class etomica.dimer.SimDimerLJadatom
-
- box - Variable in class etomica.dimer.SimDimerLJgb
-
- box - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- box - Variable in class etomica.dimer.SimDimerMEAMGB
-
- box - Variable in exception etomica.exception.ConfigurationOverlapException
-
- box - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- box - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- box - Variable in class etomica.freeenergy.npath.DataSourceEnergies
-
- box - Variable in class etomica.freeenergy.npath.SimFe
-
- box - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- box - Variable in class etomica.freeenergy.npath.SimLattice
-
- box - Variable in class etomica.freeenergy.npath.SimLJ
-
- box - Variable in class etomica.graphics.BondListener
-
- box - Variable in class etomica.graphics.DeviceNSelector
-
- box - Variable in class etomica.integrator.IntegratorBox
-
- box - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
-
- box - Variable in class etomica.integrator.mcmove.MCMoveBox
-
- box - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- box - Variable in class etomica.interfacial.FixedWall
-
- box - Variable in class etomica.interfacial.LJMC
-
- box - Variable in class etomica.interfacial.LJMD
-
- box - Variable in class etomica.interfacial.MeterWallForce
-
- box - Variable in class etomica.interfacial.MeterWallPosition
-
- box - Variable in class etomica.kmc.SimKMCLJadatom
-
- box - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- box - Variable in class etomica.liquidLJ.DataProcessorReweight
-
- box - Variable in class etomica.liquidLJ.LjMC3D
-
- box - Variable in class etomica.liquidLJ.LjMd3D
-
- box - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- box - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- box - Variable in class etomica.liquidLJ.MeterPU
-
- box - Variable in class etomica.liquidLJ.MeterPUCut
-
- box - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- box - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- box - Variable in class etomica.liquidLJ.MeterWidomInsertionP
-
- box - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
- box - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
- box - Variable in class etomica.mappedRdf.MappedRdf
-
- box - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- box - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- box - Variable in class etomica.mappedvirial.MappedU
-
- box - Variable in class etomica.mappedvirial.MappedVirialLJ
-
- box - Variable in class etomica.mappedvirial.MappedVirialLJVGr
-
- box - Variable in class etomica.mappedvirial.MeterMappedU
-
- box - Variable in class etomica.mappedvirial.MeterMappedVirial
-
- box - Variable in class etomica.mappedvirial.MeterMappedVirialV
-
- box - Variable in class etomica.mappedvirial.MeterMeanForce
-
- box - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- box - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- box - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- box - Variable in class etomica.math.numerical.CalcGradientDifferentiable
-
- box - Variable in class etomica.meam.EFSTungsten
-
- box - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- box - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- box - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- box - Variable in class etomica.meam.MEAM_MC
-
- box - Variable in class etomica.meam.MEAMMd3D
-
- box - Variable in class etomica.metastable.LJmuVT
-
- box - Variable in class etomica.metastable.LJNPT
-
- box - Variable in class etomica.metastable.LJNVT
-
- box - Variable in class etomica.metastable.MeterDensityDistribution
-
- box - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- box - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- box - Variable in class etomica.models.hexane.HexaneVolumeFraction
-
- box - Variable in class etomica.models.hexane.SimHarmonicHexane
-
- box - Variable in class etomica.models.hexane.TestHexane
-
- box - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
-
- box - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- box - Variable in class etomica.models.hexane.TestHexaneHarmonic
-
- box - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- box - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- box - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- box - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- box - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
-
- box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- box - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- box - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- box - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- box - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- box - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- box - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- box - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- box - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- box - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- box - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- box - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- box - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
-
- box - Variable in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
-
- box - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- box - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- box - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- box - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- box - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- box - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- box - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- box - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- box - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- box - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- box - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
-
- box - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- box - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
-
- box - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
-
- box - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
-
- box - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
-
- box - Variable in class etomica.models.oneDHardRods.SimWidomMode
-
- box - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- box - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- box - Variable in class etomica.models.rowley.DimerApproach
-
- box - Variable in class etomica.models.water.TestEwaldTIP4PWater
-
- box - Variable in class etomica.modifier.ModifierNMolecule
-
- box - Variable in class etomica.modules.adsorption.Adsorption
-
- box - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- box - Variable in class etomica.modules.catalysis.Catalysis
-
- box - Variable in class etomica.modules.catalysis.MeterDensityCO
-
- box - Variable in class etomica.modules.catalysis.MeterDensityCO2
-
- box - Variable in class etomica.modules.catalysis.MeterDensityO2
-
- box - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- box - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- box - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- box - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- box - Variable in class etomica.modules.chainequilibrium.MeterChainLength
-
- box - Variable in class etomica.modules.chainequilibrium.MeterConversion
-
- box - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
- box - Variable in class etomica.modules.colloid.ColloidSim
-
- box - Variable in class etomica.modules.colloid.MeterEnd2End
-
- box - Variable in class etomica.modules.crystalviewer.CrystalViewer
-
- box - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- box - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- box - Variable in class etomica.modules.droplet.Droplet
-
- box - Variable in class etomica.modules.droplet.DropletAtomic
-
- box - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- box - Variable in class etomica.modules.droplet.MeterDeformation
-
- box - Variable in class etomica.modules.ensembles.LJMC
-
- box - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- box - Variable in class etomica.modules.entropylottery.EntropyLottery
-
- box - Variable in class etomica.modules.entropylottery.MeterEntropy
-
- box - Variable in class etomica.modules.insertion.Insertion
-
- box - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- box - Variable in class etomica.modules.interfacial.InterfacialSW
-
- box - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- box - Variable in class etomica.modules.ljmd.Ljmd
-
- box - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- box - Variable in class etomica.modules.materialfracture.MeterElongation
-
- box - Variable in class etomica.modules.materialfracture.MeterLoad
-
- box - Variable in class etomica.modules.materialfracture.MeterStrain
-
- box - Variable in class etomica.modules.materialfracture.MeterStress
-
- box - Variable in class etomica.modules.materialfracture.P1Tension
-
- box - Variable in class etomica.modules.materialfracture.StrainColorScheme
-
- box - Variable in class etomica.modules.mu.MeterDensitySides
-
- box - Variable in class etomica.modules.mu.Mu
-
- box - Variable in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
-
- box - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- box - Variable in class etomica.modules.osmosis.OsmosisSim
-
- box - Variable in class etomica.modules.pistoncylinder.PistonCylinder
-
- box - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- box - Variable in class etomica.modules.render.RenderMD
-
The Box holding the atoms.
- box - Variable in class etomica.modules.rheology.MeterEndToEnd
-
- box - Variable in class etomica.modules.rheology.MeterNormalStress
-
- box - Variable in class etomica.modules.rheology.MeterViscosity
-
- box - Variable in class etomica.modules.rheology.SimulationRheology
-
- box - Variable in class etomica.modules.rosmosis.MeterFlux
-
- box - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
-
- box - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- box - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
-
- box - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- box - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
-
- box - Variable in class etomica.modules.sam.CriterionTether3
-
- box - Variable in class etomica.modules.sam.MeterTilt
-
- box - Variable in class etomica.modules.sam.MeterWallPressure
-
- box - Variable in class etomica.modules.sam.Sam
-
- box - Variable in class etomica.modules.swmd.Swmd
-
- box - Variable in class etomica.modules.vle.MeterPressure2
-
- box - Variable in class etomica.molecule.iterator.MoleculeIteratorAll
-
- box - Variable in class etomica.molecule.iterator.MpiIntraspecies1A
-
- box - Variable in class etomica.molecule.MoleculeSourceRandomMolecule
-
- box - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- box - Variable in class etomica.nbr.cell.NeighborCellManager
-
- box - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- box - Variable in class etomica.nbr.list.NeighborListManager
-
- box - Variable in class etomica.normalmode.CoordinateDefinition
-
- box - Variable in class etomica.normalmode.DeviceCellNum3DSlider
-
- box - Variable in class etomica.normalmode.DeviceCellNumXYSlider
-
- box - Variable in class etomica.normalmode.HessianDB
-
- box - Variable in class etomica.normalmode.HSDimerNPT
-
- box - Variable in class etomica.normalmode.HSNPT
-
- box - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
-
- box - Variable in class etomica.normalmode.LJVacancyMin
-
- box - Variable in class etomica.normalmode.MeterAPIPotentialEnergy
-
- box - Variable in class etomica.normalmode.MeterMaxExpansion
-
- box - Variable in class etomica.normalmode.MeterPhiDeviation
-
- box - Variable in class etomica.normalmode.MeterPlaneSlip
-
- box - Variable in class etomica.normalmode.MeterSolidDA
-
- box - Variable in class etomica.normalmode.MeterSolidDACut
-
- box - Variable in class etomica.normalmode.MeterSolidMirror
-
- box - Variable in class etomica.normalmode.MeterThetaDeviation
-
- box - Variable in class etomica.normalmode.MeterTilt
-
- box - Variable in class etomica.normalmode.MeterTiltHistogram
-
- box - Variable in class etomica.normalmode.MeterTiltRotation
-
- box - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- box - Variable in class etomica.normalmode.MeterTiltRotationStdev
-
- box - Variable in class etomica.normalmode.MinimizeHCP
-
- box - Variable in class etomica.normalmode.ModifierCells3D
-
- box - Variable in class etomica.normalmode.ModifierXCells2D
-
- box - Variable in class etomica.normalmode.ModifierYCells2D
-
- box - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- box - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- box - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- box - Variable in class etomica.normalmode.NormalModesMolecular
-
- box - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- box - Variable in class etomica.normalmode.P2XOrder
-
- box - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- box - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- box - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- box - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- box - Variable in class etomica.normalmode.SimBennet
-
- box - Variable in class etomica.normalmode.SimCalcJ
-
- box - Variable in class etomica.normalmode.SimCalcS
-
- box - Variable in class etomica.normalmode.SimCalcSLJ
-
- box - Variable in class etomica.normalmode.SimCalcSMorse
-
- box - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
-
- box - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- box - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- box - Variable in class etomica.normalmode.SimEinStep1
-
- box - Variable in class etomica.normalmode.SimEinStep1HCP
-
- box - Variable in class etomica.normalmode.SimEinStep2
-
- box - Variable in class etomica.normalmode.SimEinStep2HCP
-
- box - Variable in class etomica.normalmode.SimFluidSoftSphere
-
- box - Variable in class etomica.normalmode.SimHarmonic
-
- box - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- box - Variable in class etomica.normalmode.SimHSMDVacancy
-
- box - Variable in class etomica.normalmode.SimLJHTTISuper
-
- box - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- box - Variable in class etomica.normalmode.SimLJVacancy
-
- box - Variable in class etomica.normalmode.SimModesJ
-
- box - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- box - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- box - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- box - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- box - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- box - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- box - Variable in class etomica.normalmode.SimTarget
-
- box - Variable in class etomica.normalmode.SimTargetUmbrella
-
- box - Variable in class etomica.normalmode.SimUmbrella
-
- box - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- box - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- box - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- box - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- box - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- box - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
-
The Box holding the atoms.
- box - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
-
The Box holding the atoms.
- box - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
-
- box - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
-
- box - Variable in class etomica.potential.EwaldSummation
-
- box - Variable in class etomica.potential.EwaldSumMolecules
-
- box - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- box - Variable in class etomica.potential.Potential0Lrc
-
- box - Variable in class etomica.potential.PotentialGroup
-
- box - Variable in class etomica.rotation.DipoleBox
-
- box - Variable in class etomica.rotation.DipoleBoxMatrix
-
- box - Variable in class etomica.simulation.prototypes.ChainHSMD3D
-
- box - Variable in class etomica.simulation.prototypes.HSMC2D
-
- box - Variable in class etomica.simulation.prototypes.HSMD2D
-
- box - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- box - Variable in class etomica.simulation.prototypes.HSMD3D
-
The Box holding the atoms.
- box - Variable in class etomica.simulation.prototypes.HSMD3DNoNbr
-
- box - Variable in class etomica.simulation.prototypes.LJMD2D
-
- box - Variable in class etomica.simulation.prototypes.LJMD3D
-
- box - Variable in class etomica.simulation.prototypes.SoftSphere3d
-
- box - Variable in class etomica.simulation.prototypes.SWMD2D
-
- box - Variable in class etomica.simulation.prototypes.SWMD3D
-
- box() - Method in class etomica.simulation.Simulation
-
Convenience method to retrieve the first (and typically only) Box in the simulation.
- box - Variable in class etomica.space.Boundary
-
- box - Variable in class etomica.spin.Heisenberg
-
- box - Variable in class etomica.surfacetension.LJMC
-
- box - Variable in class etomica.surfacetension.SurfaceTensionMapped
-
- box - Variable in class etomica.tests.TestHSMD3D
-
- box - Variable in class etomica.tests.TestLJGCMC3D
-
- box - Variable in class etomica.tests.TestLJMC3D
-
- box - Variable in class etomica.tests.TestSWChain
-
- box - Variable in class etomica.thermointegration.LjMc3D
-
- box - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- box - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- box - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- box - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- box - Variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- box - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- box - Variable in class etomica.virial.simulations.SimulationVirial
-
- box - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- box - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- box - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- box - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- box - Variable in class etomica.yukawa.TestHC2YukawaMC3D
-
- box - Variable in class etomica.yukawa.TestYukawaMC3D
-
- box - Variable in class etomica.yukawa.TestYukawaMD3D
-
- box - Variable in class etomica.zeolite.ZeoliteSimulation
-
The Box holding the atoms.
- BOX - Static variable in class g3dsys.control.G3DSys
-
- Box - Class in g3dsys.images
-
Class for drawing a bounding box around the figures in molecule space
- Box(G3DSys, short) - Constructor for class g3dsys.images.Box
-
- box1 - Variable in class etomica.dimer.IntegratorDimerRT
-
- box1 - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- box1 - Variable in class etomica.simulation.prototypes.GEMCWithRotation
-
- box1 - Variable in class etomica.virial.PotentialCommonAtomic
-
- box2 - Variable in class etomica.dimer.IntegratorDimerRT
-
- box2 - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- box2 - Variable in class etomica.simulation.prototypes.GEMCWithRotation
-
- BOX_INDEX - Static variable in class etomica.util.Debug
-
index of box of interest.
- boxA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- boxA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- boxA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- boxA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- BoxAction - Interface in etomica.action
-
Elementary action performed on a Box.
- BoxActionAdapter - Class in etomica.action
-
Convenience class used to define a BoxAction.
- BoxActionAdapter() - Constructor for class etomica.action.BoxActionAdapter
-
- boxAdded(Box) - Method in class etomica.simulation.SimulationEventManager
-
- BoxAgentManager<E> - Class in etomica.box
-
Acts on behalf of client classes (a BoxAgentSource) to manage
agents for each Box in a simulation.
- BoxAgentManager(BoxAgentManager.BoxAgentSource<E>, Simulation) - Constructor for class etomica.box.BoxAgentManager
-
Constructs and sets the Simulation containing Boxes to be tracked.
- BoxAgentManager(Simulation, Function<Box, ? extends E>) - Constructor for class etomica.box.BoxAgentManager
-
- BoxAgentManager(Simulation, Function<Box, ? extends E>, Consumer<? super E>) - Constructor for class etomica.box.BoxAgentManager
-
- boxAgentManager - Variable in class etomica.nbr.CriterionSimple
-
- boxAgentManager - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- boxAgentManager - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- boxAgentManager - Variable in class etomica.nbr.PotentialMasterNbr
-
- boxAgentManager - Variable in class etomica.potential.P1HarmonicSite
-
- BoxAgentManager.BoxAgentSource<E> - Interface in etomica.box
-
Interface for an object that makes an agent to be associated with each box
upon construction.
- boxAgentSource - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- BoxAgentSourceAtomManager<E> - Class in etomica.box
-
BoxAgentSource that creates an AtomLeafAgentManager.
- BoxAgentSourceAtomManager(AtomLeafAgentManager.AgentSource<E>, Class) - Constructor for class etomica.box.BoxAgentSourceAtomManager
-
- BoxAgentSourceCellManager - Class in etomica.nbr.cell
-
BoxAgentSource responsible for creating a NeighborCellManager.
- BoxAgentSourceCellManager(Simulation, IMoleculePositionDefinition, Space) - Constructor for class etomica.nbr.cell.BoxAgentSourceCellManager
-
- BoxAgentSourceCellManagerList - Class in etomica.nbr.list
-
BoxAgentSource responsible for creating a NeighborCellManager.
- BoxAgentSourceCellManagerList(Simulation, IMoleculePositionDefinition, Space) - Constructor for class etomica.nbr.list.BoxAgentSourceCellManagerList
-
- BoxAgentSourceCellManagerListMolecular - Class in etomica.nbr.list.molecule
-
BoxAgentSource responsible for creating a NeighborCellManagerMolecular.
- BoxAgentSourceCellManagerListMolecular(Simulation, IMoleculePositionDefinition, Space) - Constructor for class etomica.nbr.list.molecule.BoxAgentSourceCellManagerListMolecular
-
- BoxAgentSourceCellManagerMolecular - Class in etomica.nbr.cell.molecule
-
BoxAgentSource responsible for creating a NeighborCellManagerMolecular.
- BoxAgentSourceCellManagerMolecular(Simulation, IMoleculePositionDefinition, Space) - Constructor for class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- BoxAgentSourceCellManagerThreaded - Class in etomica.threaded.domain
-
BoxAgentSource responsible for creating a NeighborCellManager.
- BoxAgentSourceCellManagerThreaded(Simulation, IMoleculePositionDefinition, Space) - Constructor for class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
-
- BoxAgentSourceMoleculeManager<E> - Class in etomica.box
-
BoxAgentSource that creates an MoleculeAgentManager.
- BoxAgentSourceMoleculeManager(MoleculeAgentManager.MoleculeAgentSource<E>, Simulation) - Constructor for class etomica.box.BoxAgentSourceMoleculeManager
-
- BoxAtomEvent - Class in etomica.box
-
A box event that is somehow related to an atom.
- BoxAtomEvent(Box, IAtom) - Constructor for class etomica.box.BoxAtomEvent
-
- BoxAtomIndexEvent - Class in etomica.box
-
Box event that indicates that an atom's index has changed.
- BoxAtomIndexEvent(Box, IAtom, int) - Constructor for class etomica.box.BoxAtomIndexEvent
-
- boxAtomLeafIndexChanged(BoxAtomIndexEvent) - Method in class etomica.atom.AtomLeafAgentManager
-
- boxAtomLeafIndexChanged(BoxAtomIndexEvent) - Method in interface etomica.box.BoxEventListener
-
Called when an atom's global (leaf) index has changed.
- boxAtomLeafIndexChanged(BoxAtomIndexEvent) - Method in class etomica.box.BoxEventListenerAdapter
-
- boxAtomLeafIndexChanged(BoxAtomIndexEvent) - Method in class etomica.integrator.IntegratorMD
-
- boxB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- boxB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- boxB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- boxB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- BoxCellManager - Interface in etomica.box
-
Interface for class that handles assignment of atoms to cells in a box.
- boxCells - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- BoxCluster - Class in etomica.virial
-
- BoxCluster(ClusterWeight, Space) - Constructor for class etomica.virial.BoxCluster
-
Constructor for BoxCluster.
- BoxClusterFactory() - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2.BoxClusterFactory
-
- BoxDeleteMolecules - Class in etomica.action
-
Deletes molecules from a box as determined by an AtomFilter.
- BoxDeleteMolecules(Predicate<IMolecule>) - Constructor for class etomica.action.BoxDeleteMolecules
-
- boxDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- boxDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- boxDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- boxDim - Variable in class etomica.modules.entropylottery.ModifierDimensions
-
- BoxEvent - Class in etomica.box
-
A box event fired by the box's event manager.
- BoxEvent(Box) - Constructor for class etomica.box.BoxEvent
-
- BoxEventListener - Interface in etomica.box
-
A box listener receives notifications for box events.
- BoxEventListenerAdapter - Class in etomica.box
-
- BoxEventListenerAdapter() - Constructor for class etomica.box.BoxEventListenerAdapter
-
- BoxEventManager - Class in etomica.box
-
- BoxEventManager(Box) - Constructor for class etomica.box.BoxEventManager
-
- boxFactory - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- boxGlobalAtomLeafIndexChanged(BoxIndexEvent) - Method in class etomica.atom.AtomLeafAgentManager
-
- boxGlobalAtomLeafIndexChanged(BoxIndexEvent) - Method in interface etomica.box.BoxEventListener
-
Called when the maximum leaf index in the box has changed.
- boxGlobalAtomLeafIndexChanged(BoxIndexEvent) - Method in class etomica.box.BoxEventListenerAdapter
-
- boxGlobalAtomLeafIndexChanged(BoxIndexEvent) - Method in class etomica.integrator.IntegratorMD
-
- boxH - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- boxHarmonic - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- boxHarmonic - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- boxHarmonic - Variable in class etomica.normalmode.SimOverlap
-
- boxHarmonic - Variable in class etomica.normalmode.SimOverlapLJ
-
- boxHarmonic - Variable in class etomica.normalmode.SimOverlapLJModule
-
- boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- boxHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- boxHarmonic - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- BoxImposePbc - Class in etomica.action
-
Action that imposes the central-image effect of a box having periodic
boundaries.
- BoxImposePbc(Space) - Constructor for class etomica.action.BoxImposePbc
-
Creates the action without specifying a box.
- BoxImposePbc(Box, Space) - Constructor for class etomica.action.BoxImposePbc
-
Creates the action ready to perform on the given box.
- BoxImposePbcMolecule(Box, Space) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
-
- boxIndex - Variable in class etomica.normalmode.P1ConstraintNbr
-
- BoxIndexEvent - Class in etomica.box
-
Event that conveys that the maximum leaf index in a Box has changed
(or is about to change).
- BoxIndexEvent(Box, int) - Constructor for class etomica.box.BoxIndexEvent
-
- BoxInflate - Class in etomica.action
-
Performs actions that cause volume of system to expand or contract, with
molecule positions scaled to keep them in the same relative positions.
- BoxInflate(Space) - Constructor for class etomica.action.BoxInflate
-
Constructs BoxInflate action without a box or directive to actually change
the box size.
- BoxInflate(Box, Space) - Constructor for class etomica.action.BoxInflate
-
Constructs BoxInflate action with the given box, but no directive to
actually change the box size.
- BoxInflate(Box, Space, double) - Constructor for class etomica.action.BoxInflate
-
Constructs BoxInflate action set to change the given box's density to
the given value.
- boxInflate - Variable in class etomica.liquidLJ.MeterWidomInsertionP
-
- BoxInflateAnisotropic - Class in etomica.action
-
Class that perform anisotropic angle fluctuation
- BoxInflateAnisotropic(Space) - Constructor for class etomica.action.BoxInflateAnisotropic
-
- BoxInflateAnisotropic(Box, Space) - Constructor for class etomica.action.BoxInflateAnisotropic
-
- BoxInflateDeformable - Class in etomica.action
-
Performs actions that cause volume of a deformable system to expand, with molecule
positions scaled to keep them in the same relative positions.
- BoxInflateDeformable(Space) - Constructor for class etomica.action.BoxInflateDeformable
-
- BoxInflateDeformable(Box, Space) - Constructor for class etomica.action.BoxInflateDeformable
-
- BoxInfo - Class in org.jmol.util
-
- BoxInfo() - Constructor for class org.jmol.util.BoxInfo
-
- boxK - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- boxL - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- boxLiquid - Variable in class etomica.modules.vle.VLESim
-
- boxMin - Variable in class etomica.dimer.IntegratorDimerMin
-
- boxMoleculeAdded(BoxMoleculeEvent) - Method in class etomica.atom.AtomLeafAgentManager
-
- boxMoleculeAdded(BoxMoleculeEvent) - Method in interface etomica.box.BoxEventListener
-
Called when a molecule is added to the box.
- boxMoleculeAdded(BoxMoleculeEvent) - Method in class etomica.box.BoxEventListenerAdapter
-
- boxMoleculeAdded(BoxMoleculeEvent) - Method in class etomica.integrator.IntegratorHard
-
- boxMoleculeAdded(BoxMoleculeEvent) - Method in class etomica.integrator.IntegratorMD
-
- boxMoleculeAdded(BoxMoleculeEvent) - Method in class etomica.molecule.MoleculeAgentManager
-
- BoxMoleculeCountEvent - Class in etomica.box
-
Box event that indicates the number of molecules of a particular species has
changed.
- BoxMoleculeCountEvent(Box, ISpecies, int) - Constructor for class etomica.box.BoxMoleculeCountEvent
-
- BoxMoleculeEvent - Class in etomica.box
-
A box event that is somehow related to a molecule.
- BoxMoleculeEvent(Box, IMolecule) - Constructor for class etomica.box.BoxMoleculeEvent
-
- boxMoleculeIndexChanged(BoxMoleculeIndexEvent) - Method in interface etomica.box.BoxEventListener
-
Called when an molecule's index has changed.
- boxMoleculeIndexChanged(BoxMoleculeIndexEvent) - Method in class etomica.box.BoxEventListenerAdapter
-
- boxMoleculeIndexChanged(BoxMoleculeIndexEvent) - Method in class etomica.integrator.IntegratorMD
-
- boxMoleculeIndexChanged(BoxMoleculeIndexEvent) - Method in class etomica.molecule.MoleculeAgentManager
-
- BoxMoleculeIndexEvent - Class in etomica.box
-
Box event that indicates that a molecule's index has changed.
- BoxMoleculeIndexEvent(Box, IMolecule, int) - Constructor for class etomica.box.BoxMoleculeIndexEvent
-
- boxMoleculeRemoved(BoxMoleculeEvent) - Method in class etomica.atom.AtomLeafAgentManager
-
- boxMoleculeRemoved(BoxMoleculeEvent) - Method in interface etomica.box.BoxEventListener
-
Called when a molecule is removed from the box.
- boxMoleculeRemoved(BoxMoleculeEvent) - Method in class etomica.box.BoxEventListenerAdapter
-
- boxMoleculeRemoved(BoxMoleculeEvent) - Method in class etomica.integrator.IntegratorMD
-
- boxMoleculeRemoved(BoxMoleculeEvent) - Method in class etomica.molecule.MoleculeAgentManager
-
- boxNumberMolecules(BoxMoleculeCountEvent) - Method in interface etomica.box.BoxEventListener
-
Called when the number of molecules of a particular species has changed
in the box.
- boxNumberMolecules(BoxMoleculeCountEvent) - Method in class etomica.box.BoxEventListenerAdapter
-
- boxNumberMolecules(BoxMoleculeCountEvent) - Method in class etomica.integrator.IntegratorMD
-
- boxPanel - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- BoxQuench - Class in etomica.action
-
Scales all velocities of a box so that its kinetic temperature is equal to
a given value.
- BoxQuench(int) - Constructor for class etomica.action.BoxQuench
-
- BoxQuench(double, int) - Constructor for class etomica.action.BoxQuench
-
Constructs class without specifying box and using Default temperature.
- BoxQuench(Box, double) - Constructor for class etomica.action.BoxQuench
-
Constructs class ready to perform quench on given box to given temperature.
- BoxRandomizeMomenta - Class in etomica.action
-
Randomizes the velocities of all the leaf atoms in a Box based on the
Maxwell-Boltzmann distribution.
- BoxRandomizeMomenta(Box, IRandom) - Constructor for class etomica.action.BoxRandomizeMomenta
-
- boxRef - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- boxRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- boxRef - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- boxRef - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- boxRef - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- boxRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- boxRemoved(Box) - Method in class etomica.simulation.SimulationEventManager
-
- boxScale - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
-
- BoxScaleMomenta - Class in etomica.action
-
Scales the momenta of all the leaf atoms in a Box such that the kinetic
temperature matches some value.
- BoxScaleMomenta(Box, Space) - Constructor for class etomica.action.BoxScaleMomenta
-
- boxSize - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- boxSize - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- boxSize - Variable in class etomica.potential.EwaldSummation
-
- boxSize - Variable in class etomica.potential.EwaldSumMolecules
-
- boxSize0 - Variable in class etomica.normalmode.MeterDisplacementRMS
-
- boxTarg - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
-
- boxTarg - Variable in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
-
- boxTarg - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- boxTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- boxTarget - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- boxTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- boxTarget - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- boxTarget - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- boxTarget - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- boxTarget - Variable in class etomica.normalmode.SimOverlap
-
- boxTarget - Variable in class etomica.normalmode.SimOverlapLJ
-
- boxTarget - Variable in class etomica.normalmode.SimOverlapLJModule
-
- boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- boxTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- boxTarget - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- BoxTracker() - Constructor for class etomica.integrator.IntegratorPT.BoxTracker
-
- boxVapor - Variable in class etomica.modules.vle.VLESim
-
- boxVec - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- boxWellManager - Variable in class etomica.potential.P2SquareWellRobust
-
- bpharm - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- bpharm - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- bpharmLJ - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- bpharmLJ - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- bpRes - Variable in class etomica.normalmode.MeterSolidDACut
-
- bpResDADv2 - Variable in class etomica.normalmode.MeterSolidDACut
-
- bprime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- branch - Static variable in class org.jmol.script.Token
-
- BravaisLattice - Class in etomica.lattice
-
Arbitrary-dimension Bravais Lattice, in which the sites are instances of
etomica.space.Vector, with positions given as linear combinations of a set of
primitive vectors.
- BravaisLattice(Primitive) - Constructor for class etomica.lattice.BravaisLattice
-
- BravaisLatticeCrystal - Class in etomica.lattice
-
A lattice with sites given by the "atom" sites of a crystal.
- BravaisLatticeCrystal(Primitive, Basis) - Constructor for class etomica.lattice.BravaisLatticeCrystal
-
Constructs a lattice having sites given by the "atom" sites of the given
crystal.
- BreadthFirst - Class in etomica.graph.traversal
-
- BreadthFirst() - Constructor for class etomica.graph.traversal.BreadthFirst
-
- brillouin - Static variable in class org.jmol.script.Token
-
- broadhurstBBP(int, int, int[], MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Broadhurst ladder sequence.
- broken - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
-
- broken3body - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- bScaled - Variable in class org.jmol.util.Rgb16
-
- bsDisplay - Variable in class org.jmol.util.MeshSurface
-
- bsNull - Static variable in class org.jmol.util.BitSetUtil
-
- bsPolygons - Variable in class org.jmol.util.MeshSurface
-
- bsSelectRange(Token, int) - Static method in class org.jmol.script.ScriptVariable
-
- bsSelectToken(Token) - Static method in class org.jmol.script.ScriptVariable
-
- bsSelectVar(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- bsSlabDisplay - Variable in class org.jmol.util.MeshSurface
-
- bsSlabGhost - Variable in class org.jmol.util.MeshSurface
-
- bSum - Variable in class etomica.virial.ClusterSinglyConnected
-
- buf - Variable in class etomica.util.random.RandomNumberGeneratorUnix
-
- bufferSize - Variable in class org.jmol.util.GData
-
- BuilderCollectionPotential - Class in etomica.virial.GUI.components
-
- BuilderCollectionPotential() - Constructor for class etomica.virial.GUI.components.BuilderCollectionPotential
-
- bump(IAtomList, double) - Method in class etomica.modules.adsorption.P1Wall
-
- bump(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Implements collision dynamics between two square-well atoms.
- bump(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Implements collision dynamics between two square-well atoms.
- bump(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Implements collision dynamics between two square-well atoms.
- bump(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
- bump(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
- bump(IAtomList, double) - Method in class etomica.modules.colloid.P1Wall
-
- bump(IAtomList, double) - Method in class etomica.modules.mu.P1MagicWall
-
- bump(IAtomList, double) - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Implements collision dynamics between two square-well atoms.
- bump(IAtomList, double) - Method in class etomica.modules.osmosis.P1HardWall
-
- bump(IAtomList, double) - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
-
- bump(IAtomList, double) - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
-
- bump(IAtomList, double) - Method in class etomica.normalmode.P2XOrder
-
- bump(IAtomList, double) - Method in class etomica.potential.P1HardBoundary
-
- bump(IAtomList, double) - Method in class etomica.potential.P1HardMovingBoundary
-
- bump(IAtomList, double) - Method in class etomica.potential.P1HardPeriodic
-
Performs no action.
- bump(IAtomList, double) - Method in class etomica.potential.P2DoubleWell
-
Implements collision dynamics between two square-well atoms.
- bump(IAtomList, double) - Method in class etomica.potential.P2HardAssociation
-
Implements the collision dynamics.
- bump(IAtomList, double) - Method in class etomica.potential.P2HardBond
-
Implements collision dynamics for pair attempting to separate beyond
tether distance
- bump(IAtomList, double) - Method in class etomica.potential.P2HardBondedList
-
- bump(IAtomList, double) - Method in class etomica.potential.P2HardSphere
-
Implements collision dynamics and updates lastCollisionVirial
- bump(IAtomList, double) - Method in class etomica.potential.P2HardWrapper
-
- bump(IAtomList, double) - Method in class etomica.potential.P2Ideal
-
Does nothing.
- bump(IAtomList, double) - Method in class etomica.potential.P2PenetrableBond
-
Implements collision dynamics between two square-well atoms.
- bump(IAtomList, double) - Method in class etomica.potential.P2PenetrableSphere
-
Implements collision dynamics between two penetrable-sphere atoms.
- bump(IAtomList, double) - Method in class etomica.potential.P2PenetrableSquareWell
-
Implements collision dynamics between two square-well atoms.
- bump(IAtomList, double) - Method in class etomica.potential.P2RoughSphere
-
Implements collision dynamics and updates lastCollisionVirial
Assumes atoms have same size and mass
- bump(IAtomList, double) - Method in class etomica.potential.P2SquareWell
-
Implements collision dynamics between two square-well atoms.
- bump(IAtomList, double) - Method in class etomica.potential.P2SquareWellRobust
-
Implements collision dynamics between two square-well atoms.
- bump(IAtomList, double) - Method in class etomica.potential.P2Tether
-
Implements collision dynamics for pair attempting to separate beyond tether distance
- bump(IAtomList, double) - Method in interface etomica.potential.PotentialHard
-
Implements the collision dynamics.
- button - Variable in class etomica.graphics.DeviceButton
-
- button - Variable in class etomica.zeolite.DeviceButtonSingle
-
- buttonActions - Variable in class etomica.graphics.DeviceButtonGroup
-
- buttonCorner1 - Variable in class etomica.util.Grabber
-
- buttonCorner2 - Variable in class etomica.util.Grabber
-
- buttonGroup - Variable in class etomica.graphics.DeviceButtonGroup
-
- buttonPanel - Variable in class etomica.graphics.DeviceButtonGroup
-
- buttons - Variable in class etomica.graphics.DeviceButtonGroup
-
- bv - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- bv - Variable in class etomica.models.OPLS.P2AceticAcidTwoSite
-
- bv - Variable in class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
-
- bveci - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- bveci - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- bvecj - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- bvecj - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- bveck - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- bveck - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- bVirial - Variable in class etomica.math.numerical.VirialOptimizer
-
- bVirialFromFile - Variable in class etomica.math.numerical.VirialOptimizer
-
- bvso - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- bvso - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- c - Variable in class etomica.dimer.P1LepsHarmonic
-
- c - Variable in class etomica.liquidLJ.LjMd3D.VolumeBias
-
- c - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
-
- C - Static variable in class etomica.math.Gamma
-
- c - Variable in class etomica.math.numerical.PadeApproximation
-
- c - Variable in class etomica.math.numerical.PadeApproximation.VirialParam
-
- C - Variable in class etomica.meam.PotentialEAM
-
- c - Variable in class etomica.meam.PotentialEAM_LS
-
- c - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- C - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- C - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- C - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- c - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- c - Variable in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- c - Variable in class etomica.normalmode.SoftSphereSolidEOS
-
- c - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- c - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- C - Variable in class etomica.potential.P2HePCKLJS
-
- c - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- c - Static variable in class etomica.statmech.HardSphereSolid
-
- c - Variable in class etomica.virial.ClusterPY
-
- c0 - Variable in class etomica.graphics.DisplayTable
-
- c0 - Variable in class etomica.meam.PotentialCuLREP
-
- c0 - Variable in class etomica.meam.PotentialEFS
-
- c1 - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- c1 - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- c1 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- c1 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- c1 - Variable in class etomica.meam.PotentialCuLREP
-
- c1 - Variable in class etomica.meam.PotentialEFS
-
- c1 - Variable in class etomica.modules.adsorption.EOSSWPatel
-
- c10 - Static variable in class etomica.potential.P1HydrogenMielke
-
- C10Data - Variable in class etomica.potential.P2QChemInterpolated
-
- C1CH31 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- C1CH31 - Variable in class etomica.association.BiasVolumeAceticAcid
-
- C1DBO1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- C1DBO1 - Variable in class etomica.association.BiasVolumeAceticAcid
-
- C1SBO1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- C1SBO1 - Variable in class etomica.association.BiasVolumeAceticAcid
-
- c2 - Variable in class etomica.meam.PotentialCuLREP
-
- c2 - Variable in class etomica.meam.PotentialEFS
-
- c2 - Variable in class etomica.modules.adsorption.EOSSWPatel
-
- c2 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c2_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- C2C1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- C2C1 - Variable in class etomica.association.BiasVolumeAceticAcid
-
- C2CH32 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- C2CH32 - Variable in class etomica.association.BiasVolumeAceticAcid
-
- C2DBO2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- C2DBO2 - Variable in class etomica.association.BiasVolumeAceticAcid
-
- C2SBO2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- C2SBO2 - Variable in class etomica.association.BiasVolumeAceticAcid
-
- c3 - Variable in class etomica.meam.PotentialCuLREP
-
- c3 - Variable in class etomica.meam.PotentialEFS
-
- c3 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- c3 - Variable in class etomica.modules.adsorption.EOSSWPatel
-
- c3 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- C3 - Static variable in class etomica.virial.cluster.Standard
-
- c3_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c3Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c3Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c4 - Variable in class etomica.meam.PotentialCuLREP
-
- c4 - Variable in class etomica.meam.PotentialEFS
-
- c4 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c4_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c4Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c4Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c5 - Variable in class etomica.potential.P2HydrogenHinde
-
- c5 - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- c5 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c5_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c5Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c5Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- C6 - Variable in class etomica.models.co2.P2CO2Hellmann
-
- c6 - Static variable in class etomica.potential.P1HydrogenMielke
-
- c6 - Variable in class etomica.potential.P2HydrogenHinde
-
- c6 - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- c6 - Variable in class etomica.potential.P2NitrogenHellmann
-
- c6 - Static variable in class etomica.potential.P2O2Bartolomei
-
- c6 - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c6_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- C6A - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- c6A - Static variable in class etomica.potential.P2NitrogenHellmann
-
- c6Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c6Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- C6B - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- c6B - Static variable in class etomica.potential.P2NitrogenHellmann
-
- C6BO - Static variable in class etomica.potential.P2HePCKLJS
-
- C6Data - Variable in class etomica.potential.P2QChemInterpolated
-
- c7Add - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- c7Add_sqrt - Static variable in class etomica.virial.BnJHBVArgon_Analytic
-
- C8 - Variable in class etomica.models.co2.P2CO2Hellmann
-
- c8 - Static variable in class etomica.potential.P1HydrogenMielke
-
- c8 - Variable in class etomica.potential.P2HydrogenHinde
-
- c8 - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- c8 - Static variable in class etomica.potential.P2O2Bartolomei
-
- C8A - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- C8B - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- C8Data - Variable in class etomica.potential.P2QChemInterpolated
-
- C9iso - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- C9isoSim - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- cA - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
-
- cA2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- cA2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- cA2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- cA2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- cA2nD - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- cAB - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
-
- calc(double[][]) - Method in class org.jmol.util.Eigen
-
Check for symmetry, then construct the eigenvalue decomposition
- CalcAnalytical2ndDerivativeNitrogen - Class in etomica.models.nitrogen
-
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
- CalcAnalytical2ndDerivativeNitrogen(Space, Box, P2Nitrogen, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- CalcAnalytical2ndDerivativeNitrogen(Space, Box, P2Nitrogen, CoordinateDefinitionNitrogen, boolean, double) - Constructor for class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- calcAngle(Vector, Vector) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- calcAngle(Vector, Vector) - Method in class etomica.association.BiasVolumeAceticAcid
-
- calcApprox - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
-
- calcApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- calcApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- calcApprox - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- calcApprox - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- calcApprox - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- calcApprox - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- calcApprox - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- calcAveCosThetaInitial() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- calcAveragePoint(Point3f, Point3f, Point3f) - Static method in class org.jmol.util.Measure
-
- calcAveragePointN(Point3f[], int, Point3f) - Static method in class org.jmol.util.Measure
-
- calcB2(double, double) - Static method in class etomica.modules.vle.VirialLJQB2
-
- calcBestAxisThroughPoints(Point3f[], Point3f, Vector3f, Vector3f, int) - Static method in class org.jmol.util.Measure
-
- calcBMu(double, double, double) - Static method in class etomica.metastable.LJmuVT
-
- calcBondAngleEnergy(double) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
-
- calcBondAngleEnergy(double) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- calcBondL() - Method in class etomica.models.hexane.CBMCGrowSolidHexane
-
- calcBondL() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
Returns the bond length for the new atom in a test Should take bonded
potential into account.
- calcBondTorsionalEnergy(Vector) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
-
- calcBondTorsionalEnergy(Vector) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- calcBoth(double, double) - Method in class etomica.math.Gamma
-
- calcConversion(IMoleculeList) - Method in class etomica.modules.chainequilibrium.MeterConversion
-
- calcdMudP(double, double) - Static method in class etomica.statmech.HardSphereSolid
-
- calcdmudrho(double, double) - Static method in class etomica.statmech.HardSphereSolid
-
- calcdPdrho(double, double) - Static method in class etomica.statmech.HardSphereSolid
-
- calcer - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion.MyTypeAgent
-
- calcErr(int, int) - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- calcErr(int, int) - Method in class etomica.math.numerical.AkimaSplineSmootherDy
-
- calcExternalEnergy(IAtom) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
-
- calcExternalEnergy(IAtom) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- calcF(double) - Method in class etomica.virial.MayerFunctionThreeBody
-
Returns exp(x)-1 computed directly or using a series expansion
- calcfAB(int, boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- calcfAB0(boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- calcFacs() - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- calcfC(boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- CalcFFT - Class in etomica.virial
-
CalcFFT can calculate distribution functions using FFT.
- CalcFFT(IFunction, double, int) - Constructor for class etomica.virial.CalcFFT
-
- calcForce(int, double) - Method in class etomica.threads.ThreadsMD
-
- calcfQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
This calculates all fQ values given that the entries for pairs have
already been populated.
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterSumHS
-
This calculates all FQ values given that the entries for pairs have
already been populated.
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
-
This calculates all FQ values given that the entries for pairs have
already been populated.
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS
-
This calculates all FQ values given that the entries for pairs have
already been populated.
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibody
-
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
-
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyMix
-
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoft
-
This calculates all FQ values given that the entries for pairs have
already been populated.
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBD
-
This calculates all FQ values given that the entries for pairs have
already been populated.
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
This calculates all FQ values given that the entries for pairs have
already been populated.
- calcFullFQ(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
This calculates all FQ values given that the entries for pairs have
already been populated.
- calcGageLength() - Method in class etomica.modules.materialfracture.MeterElongation
-
- calcGageLength() - Method in class etomica.modules.materialfracture.MeterStrain
-
- calcGamma(double, double) - Method in class etomica.math.Gamma
-
Return the normalized complementary incomplete gamma function,
(integral from t=x to t=inf of exp(-t)*t^(a-1)) / gamma(a) if a>0
or
(integral from t=x to t=inf of exp(-t)*t^(a-1)) * exp(x)*x^(-a) if a<=0
- calcGammaStar(double, double) - Method in class etomica.math.Gamma
-
Return the normalized incomplete gamma function,
(integral from t=0 to t=x of exp(-t)*t^(a-1)) / x^a if a>0
If a=0 and x=0, gammaStar is indeterminate and an exception is thrown.
- calcGradientDifferentiable - Variable in class etomica.dimer.SimDimerLJadatom
-
- calcGradientDifferentiable - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- calcGradientDifferentiable - Variable in class etomica.dimer.SimDimerMEAMGB
-
- calcGradientDifferentiable - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- CalcGradientDifferentiable - Class in etomica.math.numerical
-
Uses finite difference methods to determine the second order differential of the potential (i.e.
- CalcGradientDifferentiable(Box, PotentialMaster, IMoleculeList, Space) - Constructor for class etomica.math.numerical.CalcGradientDifferentiable
-
- calcGreyscaleRgbFromRgb(int) - Static method in class org.jmol.util.ColorUtil
-
Return a greyscale rgb value 0-FF using NTSC color luminance algorithm
- CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen - Class in etomica.models.nitrogen
-
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
- CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen(Space, Box, P2Nitrogen, CoordinateDefinitionNitrogen, boolean) - Constructor for class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen(Space, Box, P2Nitrogen, CoordinateDefinitionNitrogen, boolean, double, boolean) - Constructor for class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- CalcHarmonicA - Class in etomica.normalmode
-
Convenience class to calculate the Helmholtz free energy based on the
normal mode description of the system with harmonic springs governing the
system's exploration of the modes.
- CalcHarmonicA() - Constructor for class etomica.normalmode.CalcHarmonicA
-
- CalcJacobian - Class in etomica.normalmode
-
Class that calculates the dq/dx Jacobian.
- CalcJacobian() - Constructor for class etomica.normalmode.CalcJacobian
-
- calcLegendrePolynomial(int, double) - Static method in class etomica.math.SpecialFunctions
-
Calculates Pn(x), Legendre polynomial of order n for the given input value.
- calcModes - Variable in class etomica.dimer.SimDimerLJadatom
-
- calcMu - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- calcNormalizedNormal(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- CalcNumerical2ndDerivative - Class in etomica.models.nitrogen
-
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
- CalcNumerical2ndDerivative(Box, PotentialMaster, CoordinateDefinition) - Constructor for class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- CalcNumerical2ndDerivativeNitrogen - Class in etomica.models.nitrogen
-
Determine the second derivative of the atomic/ molecular potential energy w.r.t.
- CalcNumerical2ndDerivativeNitrogen(Box, P2Nitrogen, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- CalcNumerical2ndDerivativeNitrogen(Box, P2Nitrogen, CoordinateDefinitionNitrogen, boolean, double) - Constructor for class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- calcOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater3P
-
- calcOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater3P
-
- calcOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater4P
-
- calcOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater4P
-
- calcOrientation(IMolecule, IOrientationFull3D) - Method in interface etomica.molecule.OrientationCalc
-
Calculates the orientation of the given molecule and stores that
in the given orientation.
- calcOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.molecule.OrientationCalcAtom
-
- calcOrientation(IMolecule, double[]) - Method in interface etomica.molecule.OrientationCalcQuaternion
-
- calcpPade(int, int, double) - Method in class etomica.math.numerical.VirialOptimizer
-
- calcRandomBond() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
Generates a random bond.
- calcRandomBondWithAngle(IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
-
- calcRandomBondWithAngle(IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
XXX METHOD NOT TESTED! USE AT OWN PERIL! Generates a random bond that
accounts for bond angle in the calculation This method will change its
parameter.
- calcRandomBondWithAngleAndTorsion(IAtom, IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
-
- calcRandomBondWithAngleAndTorsion(IAtom, IAtom, IAtom) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
XXX METHOD NOT TESTED! USE AT OWN PERIL!l dy Generates a random bond that
accounts for bond angle and torsion in the calculation.
- calcRates() - Method in class etomica.kmc.IntegratorKMC
-
- calcRates() - Method in class etomica.kmc.IntegratorKMCCluster
-
- calcReeHoover() - Method in class etomica.virial.cluster.ClusterGenerator
-
Calculates the Ree-Hoover coefficient (coefficient for Ree-Hoover
diagram / coefficient for Mayer diagram) for mCluster and sets mCluster's
mReeHooverFactor to it.
- calcReeHooverCoefficient(Graph, int, byte) - Method in class etomica.graph.operations.ReeHoover
-
- calcRosenbluthFactors() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
Calculates wOld and wNew
- calcRosenbluthFactors() - Method in class etomica.models.hexane.MCMoveCBMC
-
- calcRotationRadius(Point3f) - Method in class g3dsys.control.G3DSys
-
Finds the atom distance furthest from the given point; for rotation
- calcScore(int[]) - Method in class etomica.virial.cluster.ClusterDiagram
-
compute a score for the cluster.
- calcSignature(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- calcSignatures() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
Compute signatures used for lookup tables of fA, fAB, fC
- calcSphereShading() - Static method in class org.jmol.util.Shader
-
- calcStartIndex() - Method in class etomica.models.hexane.CBMCGrowSolidHexane
-
- calcStartIndex() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- calcSums(IAtomList) - Method in class etomica.meam.PotentialMEAM
-
- calcSupport(AtomTypeSpheroPolyhedron, Vector) - Method in class etomica.potential.P2SpheroPolyhedron
-
- calcT(Vector, double[], double[]) - Method in class etomica.normalmode.CoordinateDefinition
-
Calculates the complex "T vector", which is collective coordinate given
by the Fourier sum (over atoms) of the generalized coordinate vector.
- calcU(IMoleculeList) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
-
- calcU(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- calcU(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- calcU(Vector) - Method in class etomica.models.nitrogen.TestRotationVector
-
- calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinition
-
Calculates the generalized coordinates for the given molecules in their
current position and orientation.
- calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionLeaf
-
Assigns the given array u to be the current position of the atom minus its lattice position
- calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
-
- calcU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- calcU(IMoleculeList) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- calculate(Box, IteratorDirective, PotentialCalculation) - Method in class etomica.dimer.PotentialMasterListDimer
-
- calculate() - Method in class etomica.models.oneDHardRods.DoubleIntegralEtas
-
- calculate(Box, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Overrides superclass method to enable direct neighbor-list iteration
instead of iteration via species/potential hierarchy.
- calculate(IMolecule, IteratorDirective.Direction, PotentialCalculation, NeighborListManagerMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- calculate(Box, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.list.PotentialMasterList
-
Overrides superclass method to enable direct neighbor-list iteration
instead of iteration via species/potential hierarchy.
- calculate(IMolecule, IteratorDirective.Direction, PotentialCalculation, NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList
-
Performs given PotentialCalculation using potentials/neighbors associated
with the given atom (if any).
- calculate(IAtom, IteratorDirective.Direction, PotentialCalculation, NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList
-
- calculate(Box, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.PotentialMasterHybrid
-
Overrides superclass method to enable direct neighbor-list iteration
instead of iteration via species/potential hierarchy.
- calculate(Box, IteratorDirective, PotentialCalculation) - Method in class etomica.nbr.site.PotentialMasterSite
-
Overrides superclass method to enable direct neighbor-list iteration
instead of iteration via species/potential hierarchy.
- calculate(IAtom, PotentialCalculation) - Method in class etomica.nbr.site.PotentialMasterSite
-
Performs given PotentialCalculation using potentials/neighbors associated
with the given atom (if any).
- calculate(MoleculesetIterator, IteratorDirective.Direction, IAtom, PotentialCalculation) - Method in class etomica.potential.PotentialGroup
-
Performs the specified calculation over the iterates given by the iterator,
using the directive to set up the iterators for the sub-potentials of this group.
- calculate(Box, IteratorDirective, PotentialCalculation) - Method in class etomica.potential.PotentialMaster
-
Performs the given PotentialCalculation on the atoms of the given Box.
- calculate(Box, IteratorDirective, PotentialCalculation) - Method in class etomica.potential.PotentialMasterLrc
-
Performs given PotentialCalculation on all LRC potentials added to this group.
- calculate(Box, IteratorDirective, PotentialCalculation) - Method in class etomica.potential.PotentialMasterMonatomic
-
- calculate(IAtom, IAtomList, int, PotentialArrayByType, IteratorDirective.Direction, PotentialCalculation) - Method in class etomica.potential.PotentialMasterMonatomic
-
- calculate(Box, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.atom.PotentialMasterListThreaded
-
- calculate(IAtom, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.atom.PotentialMasterListWorker
-
- calculate(Box, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.domain.PotentialMasterListThreaded
-
- calculate(IAtom, IteratorDirective, PotentialCalculation) - Method in class etomica.threaded.domain.PotentialMasterListWorker
-
- calculateEnergy(Box) - Method in interface etomica.normalmode.IAPIPotential
-
Returns the potential energy of the given box.
- calculateEnergy(Box) - Method in class etomica.normalmode.SimOverlapLJModule.APIPotentialReference
-
- calculateEnergy(Box) - Method in class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
-
- calculateEnergy(double) - Method in class etomica.potential.P22CLJQ
-
- calculateForces() - Method in class etomica.integrator.IntegratorGear4
-
- calculateForces() - Method in class etomica.integrator.IntegratorGear4NPH
-
- calculateLatticeDimensions(int, Vector) - Method in class etomica.config.ConfigurationLattice
-
- calculateLatticeDimensions(int, Vector) - Method in class etomica.config.ConfigurationLatticeSimple
-
- calculateLatticeDimensions(int, Vector) - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
- calculateLatticeDimensions(int, Vector) - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
- calculateLatticeDimensions(int, Vector) - Method in class etomica.threaded.domain.NeighborCellManagerThreaded
-
- calculateModes() - Method in class etomica.normalmode.NormalModesMolecular
-
- calculateModes() - Method in class etomica.normalmode.NormalModesPotential
-
- calculateModes() - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- calculateModes() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- calculateQuaternionRotation(Point3f[][], float[]) - Static method in class org.jmol.util.Measure
-
- calculateRangeIndependent(IMolecule, IteratorDirective.Direction, IAtom, PotentialCalculation) - Method in class etomica.nbr.PotentialGroupNbr
-
Performs the specified calculation over the iterates given by the iterator,
using the directive to set up the iterators for the sub-potentials of this group.
- calculateSum(FunctionData<Object>) - Method in class etomica.lattice.LatticeSum
-
- calculateSum(FunctionData<Object>) - Method in class etomica.lattice.LatticeSumCrystal
-
- calculateSum(FunctionData<Object>) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- calculateSum(LatticeSumMolecularCrystal.AtomicTensorAtomicPair) - Method in class etomica.normalmode.LatticeSumMolecularCrystal
-
- calculateSum(LatticeEnergyParacetamol) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
- calculateSystemSigmaHSRef(ModelSelectedSpecies) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- calculateSystemSigmaHSRef(IMolecularModel_SpeciesFactory[], int[]) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- calculateThreaded(Box, IteratorDirective, IPotentialCalculationThreaded, NeighborListManager) - Method in class etomica.threaded.atom.PotentialMasterListThreaded
-
- calculateThreaded(Box, IteratorDirective, IPotentialCalculationThreaded, NeighborListManager) - Method in class etomica.threaded.domain.PotentialMasterListThreaded
-
- calcV(double, double) - Method in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- calcV(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- calcValue() - Method in class etomica.virial.ClusterChainHS
-
- calcValue() - Method in class etomica.virial.ClusterChainSoft
-
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterICPYC
-
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterPY
-
- calcValue() - Method in class etomica.virial.ClusterSinglyConnected
-
- calcValue() - Method in class etomica.virial.ClusterSum
-
- calcValue() - Method in class etomica.virial.ClusterSumAssociation
-
- calcValue() - Method in class etomica.virial.ClusterSumExternalField
-
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterSumHS
-
Returns the cluster value for the given configuration.
- calcValue() - Method in class etomica.virial.ClusterSumIC
-
- calcValue() - Method in class etomica.virial.ClusterSumMultibody
-
- calcValue() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- calcValue() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- calcValue() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- calcValue() - Method in class etomica.virial.ClusterSumStickyEF
-
- calcValue(BoxCluster) - Method in interface etomica.virial.ClusterWheatley
-
Calculates the value of the configuration.
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
-
Returns the cluster value for the given configuration.
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS
-
Returns the cluster value for the given configuration.
- calcValue(BoxCluster, boolean) - Method in class etomica.virial.ClusterWheatleyHS
-
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibody
-
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
-
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyMix
-
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
Returns the cluster value for the given configuration.
- calcValue(BoxCluster, boolean) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoft
-
Returns the cluster value for the given configuration.
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBD
-
Returns the cluster value for the given configuration.
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
Returns the cluster value for the given configuration.
- calcValue(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
Returns the cluster value for the given configuration.
- CalcVibrationalModes - Class in etomica.action
-
Calculates the eigenvalues of an NxN matrix.
- CalcVibrationalModes() - Constructor for class etomica.action.CalcVibrationalModes
-
- calcVibrationalModes - Variable in class etomica.dimer.SimDimerLJadatom
-
- calcVibrationalModes - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- calcVibrationalModes - Variable in class etomica.dimer.SimDimerMEAMGB
-
- calcVibrationalModes - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- calcWeight() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- calcXs(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- calcXs(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- calcXs(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- calcXu(double, double) - Method in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- calcZbufferLimits() - Method in class g3dsys.control.G3DSys
-
- callCount - Variable in class etomica.data.meter.MeterRDF
-
- callCount - Variable in class etomica.data.meter.MeterRDFPC
-
- callCount - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- callCount - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- called - Static variable in class etomica.graph.isomorphism.Match
-
- Calorie - Class in etomica.units
-
The Joule unit of energy, equal to 1 N-m or 1 kg-m^2/s^2.
- cameradepth - Static variable in class org.jmol.script.Token
-
- cAN2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- cAN2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- cAN2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- cAN2nD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- cAN2nD - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- canAdd() - Method in class etomica.meta.properties.ArrayProperty
-
- canAdd() - Method in class etomica.meta.properties.AtomListProperty
-
- canAdd() - Method in class etomica.meta.properties.InstanceProperty
-
- canAdd() - Method in class etomica.meta.properties.MoleculeListProperty
-
- canAdd() - Method in interface etomica.meta.properties.Property
-
- canAdd() - Method in class etomica.meta.properties.VectorProperty
-
- cancelMap - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- cancelMap - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- cancelMap - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- cancelMap - Variable in class etomica.virial.cluster.VirialDiagrams
-
- cancelMap - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- cancelMap - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- cancelMap - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- cancelMap - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- cancelMap - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- cancelP - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- cancelP - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- cancelP - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- cancelP - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- cancelP - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- cancelP - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- cancelP - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- canCount() - Method in class etomica.meta.properties.ArrayProperty
-
- canCount() - Method in class etomica.meta.properties.AtomListProperty
-
- canCount() - Method in class etomica.meta.properties.InstanceProperty
-
- canCount() - Method in class etomica.meta.properties.MoleculeListProperty
-
- canCount() - Method in interface etomica.meta.properties.Property
-
- canCount() - Method in class etomica.meta.properties.VectorProperty
-
- Candela - Class in etomica.units
-
The candela is the luminous intensity, in a given direction, of a source that
emits monochromatic radiation of frequency 540 x 1012 hertz and that has a
radiant intensity in that direction of 1/683 watt per steradian.
- canDoTriangles() - Method in class org.jmol.g3d.Graphics3D
-
- canIncrement() - Method in class org.jmol.script.ScriptVariable
-
- canMoveLeft() - Method in class etomica.graph.engine.ConsoleUI
-
- canMoveRight() - Method in class etomica.graph.engine.ConsoleUI
-
- canRead() - Method in class etomica.meta.properties.ArrayProperty
-
- canRead() - Method in class etomica.meta.properties.AtomListProperty
-
- canRead() - Method in class etomica.meta.properties.InstanceProperty
-
- canRead() - Method in class etomica.meta.properties.MoleculeListProperty
-
- canRead() - Method in interface etomica.meta.properties.Property
-
- canRead() - Method in class etomica.meta.properties.VectorProperty
-
- canRemove() - Method in class etomica.meta.properties.ArrayProperty
-
- canRemove() - Method in class etomica.meta.properties.AtomListProperty
-
- canRemove() - Method in class etomica.meta.properties.InstanceProperty
-
- canRemove() - Method in class etomica.meta.properties.MoleculeListProperty
-
- canRemove() - Method in interface etomica.meta.properties.Property
-
- canRemove() - Method in class etomica.meta.properties.VectorProperty
-
- canvas - Variable in class etomica.graphics.DisplayBox
-
- canvas - Variable in class etomica.graphics.DisplayPolytope
-
- canWrite() - Method in class etomica.meta.properties.ArrayProperty
-
- canWrite() - Method in class etomica.meta.properties.AtomListProperty
-
- canWrite() - Method in class etomica.meta.properties.InstanceProperty
-
- canWrite() - Method in class etomica.meta.properties.MoleculeListProperty
-
- canWrite() - Method in interface etomica.meta.properties.Property
-
- canWrite() - Method in class etomica.meta.properties.VectorProperty
-
- cap - Static variable in class org.jmol.script.Token
-
- capAABond - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- capABBond - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- capBABond - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- capBBBond - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- capF1Bond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- capF2Bond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- capFABBond - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
-
- capFABBond - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
-
- capFABBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- capFACBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- capFACBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- capFBABond - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
-
- capFBABond - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
-
- capFBABond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- capFBCBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- capFBCBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- capFBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- capFBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- capFCABond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- capFCABond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- capFCBBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- capFCBBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- capitalize(String) - Static method in class etomica.util.Strings
-
Capitalizes the first letter of the given string.
- carbohydrate - Static variable in class org.jmol.script.Token
-
- Carbon - Class in etomica.chem.elements
-
Class for the Carbon element.
- Carbon(String) - Constructor for class etomica.chem.elements.Carbon
-
- Carbon(String, double) - Constructor for class etomica.chem.elements.Carbon
-
- cardinality() - Method in class org.jmol.util.BitSet
-
Returns the number of bits set to true in this BitSet.
- cardinalityN(int) - Method in class org.jmol.util.BitSet
-
- cardinalityOf(BitSet) - Static method in class org.jmol.util.BitSetUtil
-
cardinality = "total number of set bits"
- cartA - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- cartB - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- CartesianIterator - Class in etomica.graph.iterators
-
- CartesianIterator() - Constructor for class etomica.graph.iterators.CartesianIterator
-
- CartesianPermutator - Class in etomica.graph.iterators
-
- CartesianPermutator(int[], int[]) - Constructor for class etomica.graph.iterators.CartesianPermutator
-
- cartoon - Static variable in class org.jmol.script.Token
-
- cartoonbaseedges - Static variable in class org.jmol.script.Token
-
- cartoonfancy - Static variable in class org.jmol.script.Token
-
- cartoonrockets - Static variable in class org.jmol.script.Token
-
- CastGroupOfTablesToDataTable - Class in etomica.data.types
-
A DataProcessor that converts a homogeneous DataGroup into a multidimensional DataDoubleArray.
- CastGroupOfTablesToDataTable() - Constructor for class etomica.data.types.CastGroupOfTablesToDataTable
-
Sole constructor.
- CastGroupToDoubleArray - Class in etomica.data.types
-
A DataProcessor that converts a homogeneous DataGroup into a multidimensional DataDoubleArray.
- CastGroupToDoubleArray() - Constructor for class etomica.data.types.CastGroupToDoubleArray
-
Sole constructor.
- CastToDouble - Class in etomica.data.types
-
A DataProcessor that converts a Data instance into a DataDouble.
- CastToDouble() - Constructor for class etomica.data.types.CastToDouble
-
Sole constructor.
- CastToDoubleArray - Class in etomica.data.types
-
A DataProcessor that converts a Data instance into a DataDoubleArray.
- CastToDoubleArray() - Constructor for class etomica.data.types.CastToDoubleArray
-
Sole constructor.
- CastToGroup - Class in etomica.data.types
-
A DataProcessor that effectively wraps a Data instance into a DataGroup.
- CastToGroup() - Constructor for class etomica.data.types.CastToGroup
-
- CastToTable - Class in etomica.data.types
-
A DataProcessor that converts a Data instance into a DataTable.
- CastToTable() - Constructor for class etomica.data.types.CastToTable
-
Sole constructor.
- Catalysis - Class in etomica.modules.catalysis
-
Simulation for Catalysis module.
- Catalysis(Space, int) - Constructor for class etomica.modules.catalysis.Catalysis
-
- CatalysisAgent() - Constructor for class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
-
- CatalysisGraphic - Class in etomica.modules.catalysis
-
Catalysis graphical app.
- CatalysisGraphic(Catalysis, Space, boolean) - Constructor for class etomica.modules.catalysis.CatalysisGraphic
-
- CatalysisGraphic.Applet - Class in etomica.modules.catalysis
-
- cavityDipole - Variable in class etomica.potential.P2ReactionFieldDipole
-
- cavityDipole - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- cB - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
-
- CBMCGrowSolidHexane - Class in etomica.models.hexane
-
Contains specifics for the solid hexane model:
bond length = 0.4
rejects moving the whole molecule as a CBMC move
- CBMCGrowSolidHexane(PotentialMaster, IRandom, Space, IntegratorMC, Box, ISpecies, int) - Constructor for class etomica.models.hexane.CBMCGrowSolidHexane
-
- CBMCGrowStraightAlkane - Class in etomica.models.hexane
-
Grows a straight-chain alkane of specified length.
- CBMCGrowStraightAlkane(PotentialMaster, IRandom, IntegratorMC, Box, ISpecies, Space, int, int) - Constructor for class etomica.models.hexane.CBMCGrowStraightAlkane
-
- cbmcMove - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- cbrt(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The cube root.
- cc - Static variable in class etomica.statmech.HardSphereSolid
-
- CCbondL - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- cclec - Static variable in class etomica.potential.P2O2Bartolomei
-
- ccpol2Angles - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- ccpol2BL - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- cctMove - Variable in class etomica.models.hexane.TestHexane
-
- cctMove - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- cctMove - Variable in class etomica.models.hexane.TestSetToUHexane
-
- cdataIso - Static variable in class etomica.potential.P2HydrogenPatkowskiIso
-
- cDef - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- cDef - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- cDefR - Variable in class etomica.models.oneDHardRods.DoubleIntegralEtas
-
- cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- cDefRef - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- cDefT - Variable in class etomica.models.oneDHardRods.DoubleIntegralEtas
-
- cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- cDefTarget - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- cDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- cDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- cDim - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- cDim - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- cDim - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- cdum - Variable in class etomica.potential.P2HydrogenPatkowski
-
- cdum - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- cdz - Static variable in class etomica.statmech.HardSphereSolid
-
- ceil() - Method in class etomica.veos.bigdecimal.Rational
-
ceil(): the nearest integer not smaller than this.
- Cell - Class in etomica.nbr.cell
-
Site used to form array of cells for cell-based neighbor listing.
- Cell(int) - Constructor for class etomica.nbr.cell.Cell
-
- cell - Static variable in class org.jmol.script.Token
-
- Cell.CellFactory - Class in etomica.nbr.cell
-
- CellFactory() - Constructor for class etomica.nbr.cell.Cell.CellFactory
-
- CellFactory() - Constructor for class etomica.nbr.cell.molecule.CellMolecular.CellFactory
-
- CellLattice - Class in etomica.lattice
-
A lattice of arbitrarily-sized rectangular cells, such that a point in space can be
associated with one of the cells.
- CellLattice(Space, Vector, SiteFactory) - Constructor for class etomica.lattice.CellLattice
-
- CellLattice.NeighborIterator - Class in etomica.lattice
-
Extends the SimpleLattice neighbor iterator to provide methods that
specify the neighbor range in terms of a distance, rather than an index range.
- CellMolecular - Class in etomica.nbr.cell.molecule
-
Site used to form array of cells for cell-based neighbor listing.
- CellMolecular(int) - Constructor for class etomica.nbr.cell.molecule.CellMolecular
-
- CellMolecular.CellFactory - Class in etomica.nbr.cell.molecule
-
- cellPosition - Variable in class etomica.normalmode.CoordinateDefinition.BasisCell
-
- cellRange - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- cellRange - Variable in class etomica.nbr.cell.NeighborCellManager
-
- cells - Variable in class etomica.normalmode.CoordinateDefinition
-
- cells - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- cellSizeX - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- cellSizeX - Variable in class etomica.modules.sam.ConfigurationSAM
-
- cellSizeZ - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- cellSizeZ - Variable in class etomica.modules.sam.ConfigurationSAM
-
- CENTER - Static variable in class etomica.graphics.DisplayBox
-
- CENTER - Static variable in class etomica.graphics.DisplayPolytope
-
- center - Variable in class etomica.modules.crystalviewer.CrystalViewer
-
- center - Variable in class etomica.modules.droplet.ConfigurationDroplet
-
- center - Variable in class etomica.modules.droplet.MeterDeformation
-
- center - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- center - Variable in class etomica.molecule.MoleculePositionGeometricCenterPBC
-
- center - Static variable in class org.jmol.script.Token
-
- center - Static variable in class org.jmol.viewer.JmolConstants
-
- centerAtomColor - Variable in class etomica.modules.materialfracture.StrainColorScheme
-
- centerer - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- centerMass - Variable in class etomica.models.water.P2Water4PSoft
-
- centralImage(Vector) - Method in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
-
- centralImage(Vector) - Method in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
-
- centralImage(Vector) - Method in class etomica.space.Boundary
-
Determines the translation vector needed to apply a periodic-image
transformation that moves the given point to an image point within the
boundary (if it lies outside, in a direction subject to periodic
imaging).
- centralImage(Vector) - Method in class etomica.space.BoundaryDeformablePeriodic
-
- centralImage(Vector) - Method in class etomica.space.BoundaryRectangularNonperiodic
-
Returns a vector with all elements zero.
- centralImage(Vector) - Method in class etomica.space.BoundaryRectangularPeriodic
-
- centralImage(Vector) - Method in class etomica.space.BoundaryRectangularPore
-
- centralImage(Vector) - Method in class etomica.space.BoundaryRectangularSlit
-
- centralImage(Vector) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
-
- centralOrigin - Variable in class etomica.graphics.DisplayBox
-
Coordinate origin for central image
Explicit to 2D because drawing is done to 2D image
- centralOrigin - Variable in class etomica.graphics.DisplayPolytope
-
Coordinate origin for central image
Explicit to 2D because drawing is done to 2D image
- centrlFactNumt(int, int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
The central factorial number t(n,k) number at the indices provided.
- centrlFactNumT(int, int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
The central factorial number T(n,k) number at the indices provided.
- Ceps - Variable in class etomica.meam.P2EAM
-
- cErr - Variable in class etomica.potential.P2HePCKLJS
-
- cex - Static variable in class etomica.potential.P2HydrogenPatkowski
-
- cex - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- cexIso - Static variable in class etomica.potential.P2HydrogenPatkowskiIso
-
- cff - Variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- cgc(int, int, int, int, int, int, int) - Method in class etomica.potential.P2HydrogenPatkowski
-
- cgc(int, int, int, int, int, int, int) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- CGS - Class in etomica.units.systems
-
Centimeter-Gram-Second system of units.
- CGS() - Constructor for class etomica.units.systems.CGS
-
- CH2element - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- CH3element - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- cH3Type - Variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- cH3Type - Variable in class etomica.models.traPPE.SpeciesMethanol
-
- CH4NVT - Class in etomica.AlkaneEH
-
CH4(TraPPE-EH)
Canonical ensemble Monte Carlo simulation (NVT)
- CH4NVT(Space, int, double, double, double) - Constructor for class etomica.AlkaneEH.CH4NVT
-
- CH4NVT.Param - Class in etomica.AlkaneEH
-
- CH_ONE - Static variable in interface etomica.graph.model.Bitmap
-
- CH_ZERO - Static variable in interface etomica.graph.model.Bitmap
-
- Chain - Class in etomica.virial.cluster
-
- Chain(int) - Constructor for class etomica.virial.cluster.Chain
-
Constructor for Chain.
- chain(int) - Static method in class etomica.virial.cluster.Standard
-
Returns a chain of bonds, {{0,1},{1,2},...{n-2,n-1}}
- chain - Static variable in class org.jmol.script.Token
-
- CHAIN_TAIL - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- CHAIN_TAIL - Static variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- CHAIN_TAIL - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- CHAIN_TREE - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- chaincasesensitive - Static variable in class org.jmol.script.Token
-
- ChainedIterator - Class in etomica.graph.iterators
-
- ChainedIterator() - Constructor for class etomica.graph.iterators.ChainedIterator
-
- ChainEquilibriumGraphic - Class in etomica.modules.chainequilibrium
-
Module for chain reaction (polymerization) using ChainEquilibriumSim as the
simulation class.
- ChainEquilibriumGraphic(ChainEquilibriumSim, Space) - Constructor for class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
-
- ChainEquilibriumGraphic.Applet - Class in etomica.modules.chainequilibrium
-
- ChainEquilibriumSim - Class in etomica.modules.chainequilibrium
-
- ChainEquilibriumSim(Space) - Constructor for class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- chainFrac - Variable in class etomica.virial.ClusterChainHS
-
- chainFrac - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- chainFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- chainFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- chainFrac - Variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- chainFrac - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- chainFrac - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- chainFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- chainFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- chainFrac - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- ChainHSMD3D - Class in etomica.simulation.prototypes
-
Molecular dynamics of chains of hard spheres.
- ChainHSMD3D() - Constructor for class etomica.simulation.prototypes.ChainHSMD3D
-
- chainIterator(Iterator<Graph>) - Method in class etomica.graph.iterators.ChainedIterator
-
- chainlength - Variable in class etomica.models.hexane.MCMoveCBMC
-
- chainLength - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength.LengthAgent
-
- chainLength - Variable in class etomica.modules.colloid.ColloidSim
-
- chainLength - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- chainLength - Variable in class etomica.modules.colloid.MeterEnd2End
-
- chainLength - Variable in class etomica.modules.colloid.NeighborListManagerColloid
-
- chainLength - Variable in class etomica.modules.sam.Sam
-
- chainLengthManager - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- chainLengthManager - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- chainNumber - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical.LengthAgent
-
- ChainParameters(Parameters, Parameters) - Constructor for class etomica.graph.operations.UnaryChain.ChainParameters
-
- chainPhi - Variable in class etomica.modules.sam.Sam
-
- chainPsi - Variable in class etomica.modules.sam.Sam
-
- CHAINS - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- CHAINS - Static variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- CHAINS - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- CHAINS - Static variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- CHAINS - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- chainTheta - Variable in class etomica.modules.sam.Sam
-
- CHANGEABLE_MASK - Static variable in class org.jmol.util.Colix
-
- changeableColixMap - Variable in class org.jmol.util.GData
-
- changeableWV - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- changeableWV - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- changeableWV - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
-
- changeBox() - Method in class etomica.modules.crystalviewer.LatticeEditor
-
- changeColixArgb(short, int) - Method in class org.jmol.util.GData
-
- changeSign() - Method in class etomica.math.Complex
-
Negative of this complex number (changeSign stands for change sign).
- characterEndA - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
-
- characterEndB - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
-
- characterStartA - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
-
- characterStartB - Variable in class etomica.virial.cluster.BondConnectedSubstitutionNaphthalene.BondConnectedSubstitutionParameters2SiteNa
-
- charAt(int) - Method in class org.jmol.util.StringXBuilder
-
- Charge - Class in etomica.chem.electrostatics
-
- Charge() - Constructor for class etomica.chem.electrostatics.Charge
-
- Charge(double) - Constructor for class etomica.chem.electrostatics.Charge
-
- charge - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
-
- charge - Variable in class etomica.potential.EwaldSummation.MyCharge
-
- charge - Variable in class etomica.potential.EwaldSumMolecules.MyCharge
-
- Charge - Class in etomica.units.dimensions
-
The dimension for electrical charge.
- charge() - Method in class etomica.units.systems.CGS
-
- charge() - Method in class etomica.units.systems.LJ
-
- charge() - Method in class etomica.units.systems.MKS
-
- charge() - Method in class etomica.units.systems.UnitSystem
-
- charge() - Method in class etomica.units.systems.UnitSystem.Sim
-
- charge - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- charge2 - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
-
- ChargeAgentSourceParacetamol - Class in etomica.paracetamol
-
- ChargeAgentSourceParacetamol() - Constructor for class etomica.paracetamol.ChargeAgentSourceParacetamol
-
- ChargeAgentSourceRPM(SpeciesWater4P, boolean) - Constructor for class etomica.models.clathrates.MinimizationTIP4P.ChargeAgentSourceRPM
-
- ChargeAgentSourceTIP4PWater - Class in etomica.models.water
-
- ChargeAgentSourceTIP4PWater() - Constructor for class etomica.models.water.ChargeAgentSourceTIP4PWater
-
- chargeAll - Variable in class etomica.models.co2.PNCO2GCPM
-
- chargeC - Variable in class etomica.models.co2.PNCO2GCPM
-
- chargeC - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- chargeCC - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- chargeCC - Variable in class etomica.potential.P2CO2EMP
-
- chargeCN - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- chargeCO - Variable in class etomica.potential.P2CO2EMP
-
- chargeCP - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- chargeH - Variable in class etomica.dielectric.TIP4P_NVT
-
- chargeH - Variable in class etomica.models.water.P2Water3P
-
- chargeH - Variable in class etomica.models.water.P2Water4P
-
- chargeH - Variable in class etomica.models.water.P2WaterTIP4PHardCore
-
- chargeH - Variable in class etomica.models.water.PNWaterGCPM
-
- chargeHH - Variable in class etomica.models.water.P2Water3P
-
- chargeHH - Variable in class etomica.models.water.P2Water4P
-
- chargeHH - Variable in class etomica.models.water.P2WaterTIP4PHardCore
-
- chargeM - Variable in class etomica.dielectric.TIP4P_NVT
-
- chargeM - Variable in class etomica.models.water.P2Water4P
-
- chargeM - Variable in class etomica.models.water.P2WaterTIP4PHardCore
-
- chargeM - Variable in class etomica.models.water.PNWaterGCPM
-
- chargeMH - Variable in class etomica.models.water.P2Water4P
-
- chargeMH - Variable in class etomica.models.water.P2WaterTIP4PHardCore
-
- chargeMM - Variable in class etomica.models.water.P2Water4P
-
- chargeMM - Variable in class etomica.models.water.P2WaterTIP4PHardCore
-
- chargeN - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- chargeNN - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- chargeNP - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- chargeO - Variable in class etomica.models.co2.PNCO2GCPM
-
- chargeO - Variable in class etomica.models.water.P2Water3P
-
- chargeOH - Variable in class etomica.models.water.P2Water3P
-
- chargeOO - Variable in class etomica.models.water.P2Water3P
-
- chargeOO - Variable in class etomica.potential.P2CO2EMP
-
- chargeP - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- chargeP1 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- chargeP1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- chargeP1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- chargeP1P1 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- chargeP1P1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- chargeP1P1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- chargeP1P2 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- chargeP1P2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- chargeP1P2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- chargeP2 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- chargeP2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- chargeP2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- chargeP2P2 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- chargeP2P2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- chargeP2P2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- chargePP - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- CHbondL - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- check(Graph) - Method in class etomica.graph.property.FFTDecomposition
-
- check(Graph) - Method in class etomica.graph.property.FieldNodeCountMax
-
- check(Graph) - Method in class etomica.graph.property.HasArticulationPair
-
- check(Graph) - Method in class etomica.graph.property.HasArticulationPoint
-
- check(Graph) - Method in class etomica.graph.property.HasEdgeCount
-
- check(Graph) - Method in class etomica.graph.property.HasNodalPoint
-
- check(Graph) - Method in class etomica.graph.property.HasNoRootEdge
-
- check(Graph) - Method in class etomica.graph.property.HasSimpleArticulationPoint
-
- check(Graph) - Method in class etomica.graph.property.IsBiconnected
-
- check(Graph) - Method in class etomica.graph.property.IsConnected
-
- check(Graph) - Method in class etomica.graph.property.IsFFT
-
- check(Graph) - Method in interface etomica.graph.property.Property
-
- check() - Method in class etomica.server.health.BasicHealthCheck
-
- check() - Method in class etomica.util.TreeList
-
checks the tree for consistency of connections and ordering by sortKey.
- check(Graph) - Method in class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
-
- check(Graph) - Method in class etomica.virial.cluster.VirialDiagramsMix2.MaxIsomorphCriteriaMixture
-
- check(Graph) - Method in class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
-
- check(Graph) - Method in class etomica.virial.cluster.VirialDiagramsPT.DiscardCriteria
-
- check(Graph) - Method in class etomica.virial.IsFFT
-
- checkBox - Variable in class etomica.modules.clustergenerator.MyApplet
-
- checkBox1 - Variable in class etomica.modules.clustergenerator.MyApplet
-
- checkBox2 - Variable in class etomica.modules.clustergenerator.MyApplet
-
- checkCarbohydrate(String) - Static method in class org.jmol.viewer.JmolConstants
-
- CheckCBMCHexane - Class in etomica.models.hexane
-
- CheckCBMCHexane(Box, PotentialMaster, Space) - Constructor for class etomica.models.hexane.CheckCBMCHexane
-
- checkConfig(BoxCluster) - Method in class etomica.virial.ClusterSumHS
-
- checkConfig(BoxCluster) - Method in interface etomica.virial.ClusterWheatley
-
Determines whether the configuration is zero-valued or not.
- checkConfig(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- checkConfig(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS
-
- checkConfig(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- checkCore - Static variable in class etomica.models.co2.P2CO2H2OWheatley
-
- checkCoreCO - Static variable in class etomica.models.co2.P2CO2H2OWheatley
-
- checkDimensions() - Method in class etomica.lattice.CellLattice.NeighborIterator
-
Checks whether lattice dimensions have changed, and updates integer
neighbor range if they have.
- checkDimensions() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Checks the box's dimensions to make sure the number of cells is
appropriate.
- checkDimensions() - Method in class etomica.nbr.cell.NeighborCellManager
-
Checks the box's dimensions to make sure the number of cells is
appropriate.
- checkDimensions() - Method in class etomica.threaded.domain.NeighborCellManagerThreaded
-
- checkE - Static variable in class etomica.potential.P2ElectrostaticWithHardCore
-
- checkForSimilarSites(String[], String[], IMolecularModel_SpeciesFactory[]) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- checkGraph(Graph) - Static method in class etomica.graph.operations.DecorateWertheim3SiteRho
-
- checkIfCompatible(ModelSelectedSpecies, ModelSimulationEnvironment) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- checkIfSameSpeciesWithSimilarPotentials(IMolecularModel_SpeciesFactory, IMolecularModel_SpeciesFactory, int, int) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- checkIndexOfSpeciesSelected() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- checkme - Static variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- checkMemory() - Static method in class org.jmol.util.Logger
-
- checkMin() - Method in class etomica.kmc.IntegratorKMC
-
- checkMin() - Method in class etomica.kmc.IntegratorKMCCluster
-
- checkOHBondLength() - Method in class etomica.action.IntegratorDimerApproach
-
- checkRing(IAtom, IAtom, int) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
this function will bond atoms a & b together
- checkSet(Set<Graph>) - Static method in class etomica.graph.operations.DecorateWertheim3SiteRho
-
- checkString(String) - Static method in class etomica.units.gui.UnitFilter
-
- checkTimer(String, boolean) - Static method in class org.jmol.util.Logger
-
- checkTranslucent(boolean) - Method in class org.jmol.g3d.Graphics3D
-
- checkUnitSystemString(String) - Static method in class etomica.units.gui.UnitFilter
-
- chiData - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- chiData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- chiData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- chiData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- chiData - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- chiInfo - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- chiInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- chiInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- chiInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- chiInfo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- childCount - Variable in class etomica.species.SpeciesSpheresHetero
-
- childList - Variable in class etomica.atom.iterator.TripletInnerSequential
-
- childList - Variable in class etomica.molecule.Molecule
-
- childProps - Variable in class etomica.meta.wrappers.Wrapper
-
- children - Variable in class etomica.virial.cluster.ClusterTreeNode
-
- chiSum - Variable in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- chiSum - Variable in class etomica.integrator.mcmove.MCMoveTracker
-
- chiTag - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- chiTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- chiTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- chiTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- chiTag - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- Chlorine - Class in etomica.chem.elements
-
Class for the Chlorine element.
- Chlorine(String) - Constructor for class etomica.chem.elements.Chlorine
-
- Chlorine(String, double) - Constructor for class etomica.chem.elements.Chlorine
-
- choices() - Static method in class etomica.data.AccumulatorRatioAverageCovariance
-
- choices() - Static method in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- chooseRate() - Method in class etomica.kmc.IntegratorKMC
-
- chooseRate() - Method in class etomica.kmc.IntegratorKMCCluster
-
- Chop() - Constructor for class etomica.math.function.Function.Chop
-
Constructs with default cutoff value of 2 Double.MIN_VALUE.
- Chop(double) - Constructor for class etomica.math.function.Function.Chop
-
- chopF(MayerFunction[]) - Static method in class etomica.virial.ClusterSumStickyEF
-
- chrg3 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- chType - Variable in class etomica.virial.SpeciesAnthracene3site464
-
- chType - Variable in class etomica.virial.SpeciesAnthracene3site545
-
- chType - Variable in class etomica.virial.SpeciesPh3site464
-
- chType - Variable in class etomica.virial.SpeciesPh3site545
-
- chType - Variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- chType - Variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- chType - Variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- Circle - Class in etomica.math.geometry
-
A circle in 2D.
- Circle() - Constructor for class etomica.math.geometry.Circle
-
Creates circle with unit radius
- Circle(double) - Constructor for class etomica.math.geometry.Circle
-
Creates circle of the given radius.
- circle(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
-
- CL_OPTION_ALLOWED_SCRIPTS - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the set of allowed scripts
- CL_OPTION_ALLOWED_SCRIPTS_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_ALTERNATE_STYLESHEET - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the CSS alternate stylesheet when
converting the SVG images
- CL_OPTION_ALTERNATE_STYLESHEET_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_AOI - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the area of interest in the output
image.
- CL_OPTION_AOI_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_BACKGROUND_COLOR - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the output image's background color
- CL_OPTION_BACKGROUND_COLOR_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_CONSTRAIN_SCRIPT_ORIGIN - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to determine whether scripts a constrained to the
same origin as the document referencing them.
- CL_OPTION_CONSTRAIN_SCRIPT_ORIGIN_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_DEFAULT_FONT_FAMILY - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the default value for the font-family
CSS property when converting the SVG image
- CL_OPTION_DEFAULT_FONT_FAMILY_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_DPI - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the resolution for the output image
- CL_OPTION_DPI_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_HEIGHT - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the output image's height
- CL_OPTION_HEIGHT_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_INDEXED - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify if the PNG should be indexed.
- CL_OPTION_INDEXED_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_LANGUAGE - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the user language with which SVG
documents should be processed
- CL_OPTION_LANGUAGE_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_MAX_HEIGHT - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the output image's maximum height.
- CL_OPTION_MAX_HEIGHT_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_MAX_WIDTH - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the output image's maximum width.
- CL_OPTION_MAX_WIDTH_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_MEDIA_TYPE - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the CSS media type when converting
the SVG image
- CL_OPTION_MEDIA_TYPE_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_MIME_TYPE - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the output image's mime type
- CL_OPTION_MIME_TYPE_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_ONLOAD - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify that the converted SVG files should
be after the dispatch of the 'onload' event.
- CL_OPTION_ONLOAD_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_OUTPUT - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the output directory or file
- CL_OPTION_OUTPUT_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_QUALITY - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the output JPEG quality
- CL_OPTION_QUALITY_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_SECURITY_OFF - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to turn off secure execution of scripts
- CL_OPTION_SECURITY_OFF_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_SNAPSHOT_TIME - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify that the document should be rasterized after
seeking to the specified document time.
- CL_OPTION_SNAPSHOT_TIME_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_USER_STYLESHEET - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify an addition user stylesheet
- CL_OPTION_USER_STYLESHEET_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_VALIDATE - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify that the converted SVG files should
be validated during the conversion process.
- CL_OPTION_VALIDATE_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- CL_OPTION_WIDTH - Static variable in class etomica.graph.view.rasterizer.Main
-
Option to specify the output image's width
- CL_OPTION_WIDTH_DESCRIPTION - Static variable in class etomica.graph.view.rasterizer.Main
-
- clash - Static variable in class org.jmol.script.Token
-
- CLASSBASE_OPTIONS - Static variable in class org.jmol.viewer.JmolConstants
-
- classical - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
-
- classlist() - Static method in class etomica.units.gui.Lister
-
- className - Variable in class etomica.server.representations.ConstructionParams
-
- className - Variable in class etomica.server.representations.SimulationConstructor
-
- CLASSPATH_SCAN - Static variable in class etomica.meta.Common
-
- ClassRequirement - Class in etomica.compatibility
-
- ClathrateHarmonicFE - Class in etomica.models.clathrates
-
- ClathrateHarmonicFE(Space, int[], double, double, double[], int, String, boolean, double, boolean) - Constructor for class etomica.models.clathrates.ClathrateHarmonicFE
-
- ClathrateHarmonicFE.SimParams - Class in etomica.models.clathrates
-
- clear() - Method in class etomica.atom.AtomArrayList
-
- clear() - Method in class etomica.atom.DiameterHashByElement
-
- clear() - Method in interface etomica.graph.engine.Console
-
- clear() - Method in class etomica.graph.engine.ConsoleUI
-
- clear(Parser.Command) - Method in class etomica.graph.engine.Interpreter
-
- clear() - Method in class etomica.graph.model.GraphList
-
- clear() - Method in class etomica.modules.clustergenerator.Plot
-
Clears the plot.
- clear() - Method in class etomica.molecule.MoleculeArrayList
-
- clear() - Method in class etomica.potential.IteratorDirective
-
Puts directive in default state of no atoms specified, up direction, no
potential criteria applied, no LRC included.
- clear() - Method in class etomica.potential.P2HardBondedList.BondArrayList
-
- clear() - Method in class etomica.util.collections.IndexMap
-
- clear() - Method in class org.jmol.g3d.Graphics3D
-
- clear(int) - Method in class org.jmol.util.BitSet
-
Sets the bit specified by the index to false.
- clear() - Method in class org.jmol.util.GData
-
- clearAll() - Method in class org.jmol.util.BitSet
-
Sets all of the bits in this BitSet to false.
- clearBit(int) - Method in interface etomica.graph.model.Bitmap
-
- clearBit(int) - Method in class etomica.graph.model.impl.BitmapOfLong
-
The highest order bit is at bit 0 of bitmap, and the lowest order bit is at bit
bitSize() - 1 of bitmap.
- clearBit(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
The highest order bit is at bit 0 of bitmap[0], and the lowest order bit is at bit
bitSize() - 1 of bitmap[size()-1].
- clearBits(int, int) - Method in class org.jmol.util.BitSet
-
Sets the bits from the specified fromIndex (inclusive) to the
specified toIndex (exclusive) to false.
- clearFontCache() - Method in class org.jmol.g3d.Graphics3D
-
- clearFontCache() - Method in class org.jmol.util.GData
-
- clearNbrs() - Method in class etomica.nbr.list.AtomNeighborLists
-
Clears neighbor lists, removing all listed neighbor atoms.
- clearNbrs() - Method in class etomica.nbr.list.AtomPotentialList
-
Clears neighbor lists, resetting all flags to false (not interacting).
- clearNbrs() - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists
-
Clears neighbor lists, removing all listed neighbor molecules.
- clearNbrs() - Method in class etomica.nbr.list.molecule.MoleculePotentialList
-
Clears neighbor lists, resetting all flags to false (not interacting).
- clearRatesandEnergies() - Method in class etomica.kmc.IntegratorKMCCluster
-
- clearTags() - Method in class etomica.data.DataInfo
-
Removes all tags.
- clearTags() - Method in interface etomica.data.IDataInfo
-
Removes all tags.
- clipCode(int) - Method in class org.jmol.util.GData
-
- clipCode3(int, int, int) - Method in class org.jmol.util.GData
-
- ClipPlaneEditor - Class in etomica.modules.crystalviewer
-
Class that produces a panel with controls that presence, orientation
and position of a plane that clips atoms from the display.
- ClipPlaneEditor(Simulation, LatticePlane, DisplayBox) - Constructor for class etomica.modules.crystalviewer.ClipPlaneEditor
-
- clipPlaneEditor - Variable in class etomica.modules.crystalviewer.CrystalViewer
-
- cliqueCheck(int, int) - Method in class etomica.virial.ClusterSumHS
-
Checks to see if the set |clique| is a clique separator.
- cliqueCheck(int, int) - Method in class etomica.virial.ClusterWheatleyHS
-
Checks to see if the set |clique| is a clique separator.
- cliqueCheck(int, int) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
Checks to see if the set |clique| is a clique separator.
- cliqueCount - Variable in class etomica.virial.ClusterSumHS
-
- cliqueCount - Variable in class etomica.virial.ClusterWheatleyHS
-
- cliqueCount - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- cliqueCountE2 - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- cliqueCountEF - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- cliqueCountF1 - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- cliqueCountNone - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- cliqueList - Variable in class etomica.virial.ClusterSumHS
-
- cliqueList - Variable in class etomica.virial.ClusterWheatleyHS
-
- cliqueList - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- cliqueListE2 - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- cliqueListEF - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- cliqueListF1 - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- cliqueListNone - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- cliqueSet - Variable in class etomica.virial.ClusterSumHS
-
- cliqueSet - Variable in class etomica.virial.ClusterWheatleyHS
-
- cliqueSet - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- cliqueSetE2 - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- cliqueSetEF - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- cliqueSetF1 - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- cliqueSetNone - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- clone() - Method in interface etomica.space.Tensor
-
- clone() - Method in class etomica.space1d.Tensor1D
-
Support of implementation of Cloneable interface.
- clone() - Method in class etomica.space2d.Tensor2D
-
Support of implementation of Cloneable interface.
- clone() - Method in class etomica.space3d.Tensor3D
-
Support of implementation of Cloneable interface.
- clone() - Method in class etomica.spaceNd.TensorND
-
- clone() - Method in class etomica.util.ScientificFormat
-
- clone() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Create a copy of this.
- clone() - Method in class etomica.veos.bigdecimal.BigSurd
-
Create a deep copy.
- clone() - Method in class etomica.veos.bigdecimal.Ifactor
-
Deep copy.
- clone() - Method in class etomica.veos.bigdecimal.Rational
-
Create a copy.
- clone() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- clone() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- clone() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- clone() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- clone() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- clone() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- clone() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- clone() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- clone() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- clone() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- clone() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- clone() - Method in class org.jmol.util.BitSet
-
Cloning this BitSet produces a new BitSet that is equal to
it.
- close() - Method in interface etomica.graph.engine.Viewer
-
- close() - Method in class etomica.graph.viewer.ClusterViewer
-
- closeAlkaneView() - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- closeFile() - Method in class etomica.data.AccumulatorAverageFixedOutputFile
-
- closeFile() - Method in class etomica.data.DataLogger
-
- closeFile() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- closeFile() - Method in class etomica.zeolite.MSDCoordWriter
-
- closeFW() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
Closes file with overlap data.
- closeFW() - Method in class etomica.normalmode.MeterTargetTP
-
Closes file with overlap data.
- closeSimEnvParamView() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- closeWindow - Variable in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- CloseWindowButtonListener() - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBox.CloseWindowButtonListener
-
- cluster - Variable in class etomica.modules.clustergenerator.MyApplet
-
- cluster - Variable in class etomica.virial.ClusterMultiToSingle
-
- cluster - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
-
- cluster - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
-
- cluster - Variable in class etomica.virial.ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
-
- cluster - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
-
- cluster - Variable in class etomica.virial.MeterVirialExternalField
-
- cluster - Variable in class etomica.virial.MeterVirialExternalFieldConfined
-
- cluster - Variable in class etomica.virial.MeterVirialExternalFieldSW
-
- cluster - Variable in class etomica.virial.simulations.VirialH2OGCPMD.Clusterfoo
-
- ClusterAbstract - Interface in etomica.virial
-
- ClusterAbstractMultivalue - Interface in etomica.virial
-
- clusterAdd - Variable in class etomica.virial.ClusterDifference
-
- ClusterAssociation - Class in etomica.virial.cluster
-
- ClusterAssociation() - Constructor for class etomica.virial.cluster.ClusterAssociation
-
- clusterBD - Variable in class etomica.virial.ClusterWheatleySoft
-
- clusterBD - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- clusterBD - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- ClusterBonds - Class in etomica.virial
-
- ClusterBonds(int, int[][][]) - Constructor for class etomica.virial.ClusterBonds
-
Constructor for Cluster, with default to not using permutations (this can
be changed after construction if desired).
- ClusterBonds(int, int[][][], boolean) - Constructor for class etomica.virial.ClusterBonds
-
Constructor for Cluster.
- ClusterBonds(int[][], boolean) - Constructor for class etomica.virial.ClusterBonds
-
- ClusterBondsNonAdditive - Class in etomica.virial
-
Subclass of ClusterBonds capable of handling non-additive Mayer functions.
- ClusterBondsNonAdditive(int, int[][][], int[][]) - Constructor for class etomica.virial.ClusterBondsNonAdditive
-
Construct a ClusterBondsNonAdditive of size n, using the given list of
pair and multibonds.
- ClusterBondsNonAdditive(int[][], int[][]) - Constructor for class etomica.virial.ClusterBondsNonAdditive
-
- ClusterChainHS - Class in etomica.virial
-
This class calculates the sum of all chain and/or ring clusters for hard potentials, for which the Mayer function
can take values of only -1 or 0.
- ClusterChainHS(int, MayerFunction) - Constructor for class etomica.virial.ClusterChainHS
-
Constructs with default to perform chain-only calculation, with chainFrac = 1.0
- ClusterChainHS(int, MayerFunction, boolean) - Constructor for class etomica.virial.ClusterChainHS
-
Constructs to perform either chain-only or ring-only calculation, as directed by doRing (true for ring-only)
- ClusterChainHS(int, MayerFunction, double, double) - Constructor for class etomica.virial.ClusterChainHS
-
Constructs to perform linear combination of chain and ring values, with computed cluster values
each weighted by given fractions, and summed to get total value
- ClusterChainSoft - Class in etomica.virial
-
This class calculates the sum of all chain clusters.
- ClusterChainSoft(int, MayerFunction) - Constructor for class etomica.virial.ClusterChainSoft
-
- ClusterChainSoft(int, MayerFunction, boolean) - Constructor for class etomica.virial.ClusterChainSoft
-
- ClusterCollapsedTreeNode - Class in etomica.virial.cluster
-
- ClusterCollapsedTreeNode(int, int) - Constructor for class etomica.virial.cluster.ClusterCollapsedTreeNode
-
- ClusterCollapsedTreeNode(ClusterTreeNode, ClusterTreeNode) - Constructor for class etomica.virial.cluster.ClusterCollapsedTreeNode
-
- ClusterCoupledAtomFlipped - Class in etomica.virial
-
- ClusterCoupledAtomFlipped(ClusterAbstract, Space) - Constructor for class etomica.virial.ClusterCoupledAtomFlipped
-
- ClusterCoupledAtomFlipped(ClusterAbstract, Space, double) - Constructor for class etomica.virial.ClusterCoupledAtomFlipped
-
- ClusterCoupledFlipped - Class in etomica.virial
-
- ClusterCoupledFlipped(ClusterAbstract, Space) - Constructor for class etomica.virial.ClusterCoupledFlipped
-
cluster must have caching disabled
- ClusterCoupledFlipped(ClusterAbstract, Space, double) - Constructor for class etomica.virial.ClusterCoupledFlipped
-
cluster must have caching disabled
configurations will be flipped when the minimum distance between any two molecules
exceeds minFlipDistance.
- ClusterCoupledFlippedMultivalue - Class in etomica.virial
-
- ClusterCoupledFlippedMultivalue(ClusterAbstractMultivalue, Space, int) - Constructor for class etomica.virial.ClusterCoupledFlippedMultivalue
-
cluster must have caching disabled
- ClusterCoupledFlippedMultivalue(ClusterAbstractMultivalue, Space, double, int) - Constructor for class etomica.virial.ClusterCoupledFlippedMultivalue
-
cluster must have caching disabled
configurations will be flipped when the minimum distance between any two molecules
exceeds minFlipDistance.
- ClusterCoupledFlippedPartial - Class in etomica.virial
-
- ClusterCoupledFlippedPartial(ClusterAbstract, Space, int[][]) - Constructor for class etomica.virial.ClusterCoupledFlippedPartial
-
- clusterCriteria - Variable in class etomica.virial.ClusterSumAssociation
-
- ClusterDiagram - Class in etomica.virial.cluster
-
Holds information about a cluster diagram, including the bonds, root points,
and score.
- ClusterDiagram(int, int) - Constructor for class etomica.virial.cluster.ClusterDiagram
-
Constructs a cluster having numBody points of which numRootPoints are root points,
with bonds between each pair of points (full star).
- ClusterDiagram(int, int, int[][]) - Constructor for class etomica.virial.cluster.ClusterDiagram
-
Constructs a cluster having numBody points of which numRootPoints are root points,
with bonds as given by the array bonds.
- ClusterDiagram(int, int, int[][], Rational) - Constructor for class etomica.virial.cluster.ClusterDiagram
-
- ClusterDiagram(ClusterDiagram) - Constructor for class etomica.virial.cluster.ClusterDiagram
-
Creates a copy of the given cluster
- ClusterDiagramTree - Class in etomica.virial.cluster
-
Holds information about a cluster diagram, including the bonds, root points,
and score.
- ClusterDiagramTree(int, int) - Constructor for class etomica.virial.cluster.ClusterDiagramTree
-
Constructs a cluster having numBody points and numRootPoints root points.
- ClusterDifference - Class in etomica.virial
-
This class holds multiple clusters and returns the value from one minus the
average value from the others.
- ClusterDifference(ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.ClusterDifference
-
- ClusterExchange - Class in etomica.virial
-
- ClusterExchange(IPotentialAtomic) - Constructor for class etomica.virial.ClusterExchange
-
- Clusterfoo(ClusterAbstract, double, double) - Constructor for class etomica.virial.simulations.VirialH2OGCPMD.Clusterfoo
-
- ClusterGenerator - Class in etomica.virial.cluster
-
Generates all clusters matching certain criteria.
- ClusterGenerator(ClusterDiagram) - Constructor for class etomica.virial.cluster.ClusterGenerator
-
- ClusterICPYC - Class in etomica.virial
-
Cluster class that computes the correction to the ICPY (incrementally
corrected Percus-Yevick) formulation.
- ClusterICPYC(int, MayerFunction) - Constructor for class etomica.virial.ClusterICPYC
-
- clusterMultiBD - Variable in class etomica.virial.ClusterWheatleyMultibody
-
- clusterMultiBD - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- clusterMultiBDBD - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- ClusterMultiToSingle - Class in etomica.virial
-
- ClusterMultiToSingle(ClusterAbstractMultivalue, int) - Constructor for class etomica.virial.ClusterMultiToSingle
-
- ClusterOperations - Class in etomica.virial.cluster
-
- ClusterOperations() - Constructor for class etomica.virial.cluster.ClusterOperations
-
- ClusterPanel - Class in etomica.modules.clustergenerator
-
- ClusterPanel(ClusterDiagram, boolean, boolean, boolean, boolean, boolean) - Constructor for class etomica.modules.clustergenerator.ClusterPanel
-
- ClusterPY - Class in etomica.virial
-
- ClusterPY(int, MayerFunction) - Constructor for class etomica.virial.ClusterPY
-
- clusterRadius - Variable in class etomica.dimer.SimDimerMEAMGB
-
- ClusterRetrievePrimes(ClusterWheatleyMultibodyDerivatives, int) - Constructor for class etomica.virial.ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
-
- ClusterRetrievePrimes(ClusterWheatleyMultibodyDerivativesBD, int) - Constructor for class etomica.virial.ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
-
- ClusterRetrievePrimes(ClusterWheatleySoftDerivatives, int) - Constructor for class etomica.virial.ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
-
- ClusterRetrievePrimes(ClusterWheatleySoftDerivativesBD, int) - Constructor for class etomica.virial.ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
-
- clusters - Variable in class etomica.virial.ClusterSum
-
- clusters - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- clusters - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- clusters - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- clusters - Variable in class etomica.virial.MeterVirial
-
- clusters - Variable in class etomica.virial.MeterVirialBD
-
- clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfined
-
- clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
-
- clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
-
- clusters - Variable in class etomica.virial.MeterVirialExternalFieldOverlapRho
-
- clusters - Variable in class etomica.virial.MeterVirialExternalFieldRho
-
- clusters - Variable in class etomica.virial.MeterVirialSWWE
-
- ClusterSinglyConnected - Class in etomica.virial
-
This class calculates the sum of all tree clusters using an adaptation of Wheatley's
recursive formulation.
- ClusterSinglyConnected(int, MayerFunction) - Constructor for class etomica.virial.ClusterSinglyConnected
-
- clusterSubtract - Variable in class etomica.virial.ClusterDifference
-
- ClusterSum - Class in etomica.virial
-
- ClusterSum(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSum
-
Constructor for ClusterSum.
- ClusterSumAssociation - Class in etomica.virial
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's double attraction-site model, hyper-point diagram
2 F-bond, 1 f_R bond diagram
- ClusterSumAssociation(ClusterBonds[], double[], MayerFunction[], ClusterSumAssociation.ClusterCriteria) - Constructor for class etomica.virial.ClusterSumAssociation
-
Constructor for ClusterSum.
- ClusterSumAssociation.ClusterCriteria - Interface in etomica.virial
-
- ClusterSumEF - Class in etomica.virial
-
- ClusterSumEF(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumEF
-
Constructs a Cluster sum of the given cluster and weights.
- ClusterSumExternalField - Class in etomica.virial
-
- ClusterSumExternalField(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumExternalField
-
- ClusterSumHS - Class in etomica.virial
-
This class calculates the sum of all biconnected clusters for hard spheres.
- ClusterSumHS(ClusterBonds[], double[], MayerFunction) - Constructor for class etomica.virial.ClusterSumHS
-
- ClusterSumIC - Class in etomica.virial
-
- ClusterSumIC(ClusterBonds[], double[], MayerFunction[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumIC
-
- ClusterSumIC.FR2 - Class in etomica.virial
-
- ClusterSumMultibody - Class in etomica.virial
-
Cluster class capable of computing multibody (up to 6th order) contributions
to diagrams.
- ClusterSumMultibody(ClusterBonds[], double[], MayerFunction[], MayerFunctionNonAdditive[]) - Constructor for class etomica.virial.ClusterSumMultibody
-
- ClusterSumMultibodyShell - Class in etomica.virial
-
- ClusterSumMultibodyShell(ClusterSumMultibody, ClusterBonds[], double[], MayerFunction[], MayerFunctionNonAdditive[]) - Constructor for class etomica.virial.ClusterSumMultibodyShell
-
Constructs a cluster (shell) that depends on another ClusterSumMultibody instance
(the core) to do the actual work of calculating all the f values.
- ClusterSumNonAdditiveTrimerEnergy - Class in etomica.virial
-
- ClusterSumNonAdditiveTrimerEnergy(ClusterBonds[], double[], MayerFunction[], Potential) - Constructor for class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
Adapted by Kate from ClusterSumPolarizable (simplification for nonadditive trimer energy only).
- ClusterSumPolarizable - Class in etomica.virial
-
- ClusterSumPolarizable(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizable
-
Constructor for ClusterSum.
- ClusterSumPolarizableWertheimProduct - Class in etomica.virial
-
- ClusterSumPolarizableWertheimProduct(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizableWertheimProduct
-
Constructor for ClusterSum for Wertheim diagram including multi body term.
- ClusterSumPolarizableWertheimProduct4Pt - Class in etomica.virial
-
- ClusterSumPolarizableWertheimProduct4Pt(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
Constructor for ClusterSum for Wertheim diagram including multi body term.
- ClusterSumPolarizableWertheimProduct4PtFinal - Class in etomica.virial
-
- ClusterSumPolarizableWertheimProduct4PtFinal(ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
Constructor for ClusterSum for Wertheim diagram including multi body term.
- ClusterSumShell - Class in etomica.virial
-
- ClusterSumShell(ClusterSum, ClusterBonds[], double[], MayerFunction[]) - Constructor for class etomica.virial.ClusterSumShell
-
Constructs a cluster (shell) that depends on another ClusterSum instance
(the core) to do the actual work of calculating all the f values.
- ClusterSumStickyEF - Class in etomica.virial
-
- ClusterSumStickyEF(ClusterBonds[], double[], MayerFunction[], ClusterSumStickyEF[], IRandom) - Constructor for class etomica.virial.ClusterSumStickyEF
-
- ClusterSumStickyEF(ClusterSumEF, ClusterSumStickyEF[], IRandom) - Constructor for class etomica.virial.ClusterSumStickyEF
-
- ClusterTree - Class in etomica.virial
-
- ClusterTree(ClusterDiagramTree, MayerFunction[]) - Constructor for class etomica.virial.ClusterTree
-
- ClusterTreeBonds - Class in etomica.virial
-
- ClusterTreeBonds() - Constructor for class etomica.virial.ClusterTreeBonds
-
- ClusterTreeEF - Class in etomica.virial
-
- ClusterTreeEF(ClusterDiagramTree, MayerFunction[]) - Constructor for class etomica.virial.ClusterTreeEF
-
- ClusterTreeNode - Class in etomica.virial.cluster
-
- ClusterTreeNode(int) - Constructor for class etomica.virial.cluster.ClusterTreeNode
-
- ClusterViewer - Class in etomica.graph.viewer
-
- ClusterWeight - Interface in etomica.virial
-
- ClusterWeight.Factory - Interface in etomica.virial
-
- ClusterWeightAbs - Class in etomica.virial
-
- ClusterWeightAbs(ClusterAbstract) - Constructor for class etomica.virial.ClusterWeightAbs
-
- clusterWeights - Variable in class etomica.virial.ClusterSum
-
- clusterWeights - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- clusterWeights - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- clusterWeights - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- ClusterWeightSumWall - Class in etomica.virial
-
- ClusterWeightSumWall(ClusterWeightSumWall.DataSourceClusterWall, int) - Constructor for class etomica.virial.ClusterWeightSumWall
-
- ClusterWeightSumWall.DataSourceClusterWall - Interface in etomica.virial
-
- ClusterWeightUmbrella - Class in etomica.virial
-
Umbrella cluster weight wrapper function.
- ClusterWeightUmbrella(ClusterAbstract[]) - Constructor for class etomica.virial.ClusterWeightUmbrella
-
Contructs an umbrella cluster from the given clusters.
- ClusterWheatley - Interface in etomica.virial
-
- clusterWheatleyBDBD - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
-
- ClusterWheatleyExtendSW - Class in etomica.virial
-
- ClusterWheatleyExtendSW(int, MayerFunction, MayerFunction) - Constructor for class etomica.virial.ClusterWheatleyExtendSW
-
- ClusterWheatleyHS - Class in etomica.virial
-
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
- ClusterWheatleyHS(int, MayerFunction) - Constructor for class etomica.virial.ClusterWheatleyHS
-
- ClusterWheatleyHS.AllSigs - Class in etomica.virial
-
- ClusterWheatleyMultibody - Class in etomica.virial
-
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in non-additive contributions.
- ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive[]) - Constructor for class etomica.virial.ClusterWheatleyMultibody
-
- ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive) - Constructor for class etomica.virial.ClusterWheatleyMultibody
-
- ClusterWheatleyMultibody(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], double) - Constructor for class etomica.virial.ClusterWheatleyMultibody
-
- ClusterWheatleyMultibodyBD - Class in etomica.virial
-
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in non-additive contributions.
- ClusterWheatleyMultibodyBD(int, MayerFunction, MayerFunctionNonAdditive[], int) - Constructor for class etomica.virial.ClusterWheatleyMultibodyBD
-
- ClusterWheatleyMultibodyBD(int, MayerFunction, MayerFunctionNonAdditive, int) - Constructor for class etomica.virial.ClusterWheatleyMultibodyBD
-
- ClusterWheatleyMultibodyBD(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], int) - Constructor for class etomica.virial.ClusterWheatleyMultibodyBD
-
- ClusterWheatleyMultibodyDerivatives - Class in etomica.virial
-
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in non-additive contributions.
- ClusterWheatleyMultibodyDerivatives(int, MayerFunction, MayerFunctionNonAdditive[], double, int, boolean) - Constructor for class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- ClusterWheatleyMultibodyDerivatives(int, MayerFunction, MayerFunctionNonAdditive, double, int, boolean) - Constructor for class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- ClusterWheatleyMultibodyDerivatives(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], double, int, boolean) - Constructor for class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes - Class in etomica.virial
-
- ClusterWheatleyMultibodyDerivativesBD - Class in etomica.virial
-
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams, but adds in non-additive contributions.
- ClusterWheatleyMultibodyDerivativesBD(int, MayerFunction, MayerFunctionNonAdditive, MayerFunctionNonAdditive[], int, int, boolean) - Constructor for class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes - Class in etomica.virial
-
- ClusterWheatleyMultibodyMix - Class in etomica.virial
-
This class uses Wheatley's recursion approach to calculating all biconnected
diagrams for a mixture, but adds in 3-body contributions.
- ClusterWheatleyMultibodyMix(int, int[], MayerFunction[][], MayerFunctionNonAdditive[][][], double, boolean) - Constructor for class etomica.virial.ClusterWheatleyMultibodyMix
-
Constructs a cluster capable of handling mixtures of nonadditive
molecules.
- ClusterWheatleyPartitionScreening - Class in etomica.virial
-
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
- ClusterWheatleyPartitionScreening(int, MayerFunction) - Constructor for class etomica.virial.ClusterWheatleyPartitionScreening
-
- ClusterWheatleyPartitionScreening(int, MayerFunction, int) - Constructor for class etomica.virial.ClusterWheatleyPartitionScreening
-
- ClusterWheatleyPartitionScreening.FrequencyCounter - Class in etomica.virial
-
- ClusterWheatleySoft - Class in etomica.virial
-
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
- ClusterWheatleySoft(int, MayerFunction, double) - Constructor for class etomica.virial.ClusterWheatleySoft
-
- ClusterWheatleySoftBD - Class in etomica.virial
-
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
- ClusterWheatleySoftBD(int, MayerFunction, int) - Constructor for class etomica.virial.ClusterWheatleySoftBD
-
- ClusterWheatleySoftBDMix - Class in etomica.virial
-
Cluster class using Whealtey's recursion with BigDecimal to handle mixtures.
- ClusterWheatleySoftBDMix(int, int[], MayerFunction[][], int) - Constructor for class etomica.virial.ClusterWheatleySoftBDMix
-
- ClusterWheatleySoftDerivatives - Class in etomica.virial
-
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
- ClusterWheatleySoftDerivatives(int, MayerFunction, double, int) - Constructor for class etomica.virial.ClusterWheatleySoftDerivatives
-
- ClusterWheatleySoftDerivatives.ClusterRetrievePrimes - Class in etomica.virial
-
- ClusterWheatleySoftDerivativesBD - Class in etomica.virial
-
This class calculates the sum of all biconnected clusters using Wheatley's
recursive formulation.
- ClusterWheatleySoftDerivativesBD(int, MayerFunction, int, int) - Constructor for class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes - Class in etomica.virial
-
- ClusterWheatleySoftMix - Class in etomica.virial
-
Cluster class using Whealtey's recursion to handle mixtures.
- ClusterWheatleySoftMix(int, int[], MayerFunction[][], double) - Constructor for class etomica.virial.ClusterWheatleySoftMix
-
- cm - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- cm2ndD - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- Cmax - Variable in class etomica.meam.ParameterSetMEAM
-
- Cmin - Variable in class etomica.meam.ParameterSetMEAM
-
- cmtoau - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- cmzFix - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- cn - Variable in class etomica.potential.P3HydrogenManzhos
-
- CO - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- coef - Variable in class etomica.potential.P2HydrogenHinde
-
- coef - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- Coefficient - Interface in etomica.graph.model
-
- coefficient() - Method in interface etomica.graph.model.Graph
-
- coefficient() - Method in class etomica.graph.model.impl.GraphImpl
-
- coefficient - Variable in class etomica.virial.cluster.ClusterTreeNode
-
- coefficient_fourier - Variable in class etomica.potential.EwaldSumMolecules
-
- CoefficientImpl - Class in etomica.graph.model.impl
-
- CoefficientImpl(int) - Constructor for class etomica.graph.model.impl.CoefficientImpl
-
- CoefficientImpl(int, int) - Constructor for class etomica.graph.model.impl.CoefficientImpl
-
- CoefficientImpl(int, int, double) - Constructor for class etomica.graph.model.impl.CoefficientImpl
-
- coefficients - Variable in class etomica.normalmode.WaveVectorFactory1D
-
- coefficients - Variable in class etomica.normalmode.WaveVectorFactory2D
-
- coefficients - Variable in class etomica.normalmode.WaveVectorFactoryFcc
-
- coefficients - Variable in class etomica.normalmode.WaveVectorFactorySimple
-
- coefficients - Variable in class etomica.virial.MayerFunctionProductGeneral
-
- coefficients - Variable in class etomica.virial.MayerFunctionSum
-
- coefficients - Variable in class etomica.virial.MayerFunctionSumGeneral
-
- coeffQ(int) - Method in class etomica.veos.QSeries
-
Computes coefficients of the polynomial in volume for Q for the given N.
- coeffs - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- coeffs - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- coeffs - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- Colix - Class in org.jmol.util
-
Implements a color index model using a colix as a
COLor IndeX.
- Colix() - Constructor for class org.jmol.util.Colix
-
- colix - Variable in class org.jmol.util.MeshSurface
-
- colixBack - Variable in class org.jmol.util.MeshSurface
-
- colixCurrent - Variable in class org.jmol.util.GData
-
- collapse() - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- collapseBlocks() - Method in class etomica.data.AccumulatorAverageCollapsing
-
- collapseData(double) - Method in class etomica.data.histogram.HistogramCollapsing
-
Collapses existing data and expands x range sufficiently so that the
given x value is within the range of the histogram.
- collapseData() - Method in class etomica.data.history.HistoryCollapsing
-
- collapseData() - Method in class etomica.data.history.HistoryCollapsingAverage
-
- collapseData() - Method in class etomica.data.history.HistoryCollapsingDiscard
-
- CollectionBondedPotentialAlcohols - Class in etomica.virial.GUI.components
-
- CollectionBondedPotentialAlcohols() - Constructor for class etomica.virial.GUI.components.CollectionBondedPotentialAlcohols
-
- CollectionBondedPotentialAlkanes - Class in etomica.virial.GUI.components
-
- CollectionBondedPotentialAlkanes(int) - Constructor for class etomica.virial.GUI.components.CollectionBondedPotentialAlkanes
-
- CollectionPotentialAtomicLike - Class in etomica.virial.GUI.components
-
- CollectionPotentialAtomicLike(int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- CollectionPotentialAtomicUnlike - Class in etomica.virial.GUI.components
-
- CollectionPotentialAtomicUnlike(int, int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- CollectionPotentialMolecularLike - Class in etomica.virial.GUI.components
-
- CollectionPotentialMolecularLike(int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialMolecularLike
-
- CollectionPotentialMolecularUnlike - Class in etomica.virial.GUI.components
-
- CollectionPotentialMolecularUnlike(int, int) - Constructor for class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- collector - Variable in class etomica.modules.statistics.DataAccPusher
-
- colliderAgent - Variable in class etomica.integrator.IntegratorHard
-
- colliderAgent() - Method in class etomica.integrator.IntegratorHard
-
- colliderColor - Variable in class etomica.graphics.ColorSchemeColliders
-
Color applied to the downList atom of the colliding pair
- collisionAction(IntegratorHard.Agent) - Method in class etomica.data.DataSourceTensorVirialHard
-
Sums contribution to virial for each collision.
- collisionAction(IntegratorHard.Agent) - Method in class etomica.data.meter.MeterPressureHard
-
Implementation of CollisionListener interface
Adds collision virial (from potential) to accumulator
- collisionAction(IntegratorHard.Agent) - Method in class etomica.data.meter.MeterPressureHardTensor
-
- collisionAction(IntegratorHard.Agent) - Method in interface etomica.integrator.IntegratorHard.CollisionListener
-
- collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
Implementation of CollisionListener interface
Adds collision virial (from potential) to accumulator
- collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.catalysis.InteractionTracker
-
- collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
Sums contribution to virial for each collision.
- collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.mu.DataSourceWallPressureMu
-
Implementation of CollisionListener interface
Adds collision virial (from potential) to accumulator
- collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.osmosis.MeterOsmoticPressure
-
- collisionAction(IntegratorHard.Agent) - Method in class etomica.modules.pistoncylinder.DataSourceWallPressure
-
Implementation of CollisionListener interface
Adds collision virial (from potential) to accumulator
- collisionCount - Variable in class etomica.integrator.IntegratorHard
-
- collisionDiameter - Variable in class etomica.potential.P2HardSphere
-
Separation at which spheres first overlap
- collisionHandlerDown - Variable in class etomica.integrator.IntegratorHard
-
- collisionHandlerUp - Variable in class etomica.integrator.IntegratorHard
-
- CollisionHandlerUp() - Constructor for class etomica.integrator.IntegratorHard.CollisionHandlerUp
-
- collisionPartner - Variable in class etomica.integrator.IntegratorHard.Agent
-
- collisionPartner() - Method in class etomica.integrator.IntegratorHard.Agent
-
- collisionPotential - Variable in class etomica.integrator.IntegratorHard.Agent
-
- collisionTime() - Method in class etomica.integrator.IntegratorHard.Agent
-
Accessor method for the time to next collision of this atom
- collisionTime(IAtomList, double) - Method in class etomica.modules.adsorption.P1Wall
-
- collisionTime(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
Computes next time of collision of the two atoms, assuming free-flight
kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
Computes next time of collision of the two atoms, assuming free-flight
kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.modules.colloid.P1Wall
-
- collisionTime(IAtomList, double) - Method in class etomica.modules.colloid.P2HardSphereMC
-
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.modules.colloid.P2SquareWellMonomer
-
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.modules.mu.P1MagicWall
-
- collisionTime(IAtomList, double) - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.modules.osmosis.P1HardWall
-
- collisionTime(IAtomList, double) - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
-
Computes next time of collision of the two atoms, assuming free-flight
kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
-
- collisionTime(IAtomList, double) - Method in class etomica.normalmode.P2XOrder
-
- collisionTime(IAtomList, double) - Method in class etomica.potential.P1HardBoundary
-
- collisionTime(IAtomList, double) - Method in class etomica.potential.P1HardMovingBoundary
-
- collisionTime(IAtomList, double) - Method in class etomica.potential.P1HardPeriodic
-
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2DoubleWell
-
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardAssociation
-
Computes the next time of collision of the given atomPair assuming free flight.
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardBond
-
Time at which two atoms will reach the end of their tether, assuming
free-flight kinematics
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardBondedList
-
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardSphere
-
Time to collision of pair, assuming free-flight kinematics
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2HardWrapper
-
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2Ideal
-
Returns Double.POSITIVE_INFINITY.
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2PenetrableBond
-
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2PenetrableSphere
-
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2PenetrableSquareWell
-
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2SquareWell
-
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2SquareWellRobust
-
Computes next time of collision of two square-well atoms, assuming free-flight kinematics.
- collisionTime(IAtomList, double) - Method in class etomica.potential.P2Tether
-
Time at which two atoms will reach the end of their tether, assuming free-flight kinematics
- collisionTime(IAtomList, double) - Method in interface etomica.potential.PotentialHard
-
Computes the time of collision of the given atom(s) with the hard
potential, assuming no intervening collisions.
- collisionTimeStep - Variable in class etomica.integrator.IntegratorHard
-
- collisionValue(IntegratorHard.Agent) - Method in class etomica.data.DataSourceTensorVirialHard
-
Contribution to the virial from the most recent collision of the given pair/potential.
- collisionValue(IntegratorHard.Agent) - Method in interface etomica.data.meter.DataSourceCollisional
-
- collisionValue(IntegratorHard.Agent) - Method in class etomica.data.meter.MeterPressureHard
-
Implementation of Meter.MeterCollisional interface.
- colloidDensityProfileMeter - Variable in class etomica.modules.colloid.ColloidGraphic
-
- ColloidGraphic - Class in etomica.modules.colloid
-
Colloid module app.
- ColloidGraphic(ColloidSim, Space) - Constructor for class etomica.modules.colloid.ColloidGraphic
-
- ColloidGraphic.Applet - Class in etomica.modules.colloid
-
- ColloidGraphic.GraftAction - Class in etomica.modules.colloid
-
- ColloidGraphic.WallRangeModifier - Class in etomica.modules.colloid
-
- colloidMonomerBondManager - Variable in class etomica.modules.colloid.ColloidSim
-
- colloidMonomerBondManager - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- ColloidSim - Class in etomica.modules.colloid
-
Colloid simulation.
- ColloidSim(Space) - Constructor for class etomica.modules.colloid.ColloidSim
-
- ColloidSim.CriterionNone - Class in etomica.modules.colloid
-
- color - Variable in class etomica.association.ColorSchemeSmer.ColorAgent
-
- color - Variable in class etomica.graph.operations.Decorate.DecorateParameters
-
- color() - Method in class etomica.graph.operations.DeleteEdgeParameters
-
- color() - Method in class etomica.graph.operations.DifByConstant.DifByConstantParameters
-
- color() - Method in class etomica.graph.operations.DifParameters
-
- color - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedSite
-
- color - Variable in class g3dsys.images.Bond
-
- color - Static variable in class org.jmol.script.Token
-
- color1 - Variable in class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
-
- COLOR_0 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_1 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_10 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_11 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_12 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_2 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_3 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_4 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_5 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_6 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_7 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_8 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_9 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODE_0 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODE_1 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODE_2 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODE_3 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODE_4 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODE_5 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODE_6 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODE_7 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODE_8 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODE_9 - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODE_DEFAULT - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_CODES - Static variable in interface etomica.graph.model.Metadata
-
- COLOR_MAP - Static variable in interface etomica.graph.model.Metadata
-
- ColorAgent() - Constructor for class etomica.association.ColorSchemeSmer.ColorAgent
-
- colorAllAtoms() - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- colorAllAtoms() - Method in interface etomica.graphics.ColorSchemeCollective
-
Determine color of all atoms.
- colorAllAtoms() - Method in class etomica.graphics.ColorSchemeCollectiveAgent
-
- colorAllAtoms() - Method in class etomica.graphics.ColorSchemeCoordination
-
- colorAllAtoms() - Method in class etomica.graphics.ColorSchemeNeighbor
-
- colorAllAtoms() - Method in class etomica.graphics.ColorSchemeNeighborCell
-
- colorAllAtoms() - Method in class etomica.graphics.ColorSchemeOverlap
-
- colorAllAtoms() - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- colorAllAtoms() - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
-
- colorAllAtoms() - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- colorAllAtoms() - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- colorCounts - Variable in class etomica.graph.model.comparators.ComparatorNodeColors
-
- colorMaps - Variable in class etomica.modules.chainequilibrium.ColorSchemeStepWise
-
- colorNew() - Method in class etomica.graph.operations.DifByConstant.DifByConstantParameters
-
- ColorOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.ColorOptionHandler
-
- colorPointFromInt(int, Point3f) - Static method in class org.jmol.util.ColorUtil
-
- colorPointFromInt2(int) - Static method in class org.jmol.util.ColorUtil
-
- colorPointFromString(String, Point3f) - Static method in class org.jmol.util.ColorUtil
-
- colorPtToInt(Point3f) - Static method in class org.jmol.util.ColorUtil
-
- colorrasmol - Static variable in class org.jmol.script.Token
-
- colors - Variable in class etomica.association.ColorSchemeSmerByLength
-
- colors - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- colors - Variable in class etomica.graph.model.comparators.ComparatorNodeColors
-
- COLORS - Static variable in interface etomica.graph.model.Metadata
-
- colors - Variable in class etomica.graphics.ColorSchemeOverlap
-
- colors - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- colorScheme - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.AtomFilterDeviation
-
- colorScheme - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- ColorScheme - Class in etomica.graphics
-
Class that defines the algorithm used to determine atoms colors when drawn to DisplayBox.
- ColorScheme() - Constructor for class etomica.graphics.ColorScheme
-
- ColorScheme(Color) - Constructor for class etomica.graphics.ColorScheme
-
- colorScheme - Variable in class etomica.graphics.DisplayBox
-
- colorScheme - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- ColorScheme.Simple - Class in etomica.graphics
-
Colors all atoms with baseColor.
- ColorSchemeByType - Class in etomica.graphics
-
Colors the atom according to the color given by its type field.
- ColorSchemeByType() - Constructor for class etomica.graphics.ColorSchemeByType
-
- ColorSchemeCell - Class in etomica.graphics
-
- ColorSchemeCell(PotentialMasterNbr, IRandom, Box) - Constructor for class etomica.graphics.ColorSchemeCell
-
- ColorSchemeCollective - Interface in etomica.graphics
-
- ColorSchemeCollectiveAgent - Class in etomica.graphics
-
Parent class for color schemes that are best implemented by attaching colors
to all atoms at once, rather than determining the color of each as it is drawn.
- ColorSchemeCollectiveAgent(Box) - Constructor for class etomica.graphics.ColorSchemeCollectiveAgent
-
- ColorSchemeColliders - Class in etomica.graphics
-
This colorScheme acts to color differently the two atoms that are scheduled to collide next.
- ColorSchemeColliders(IntegratorHard) - Constructor for class etomica.graphics.ColorSchemeColliders
-
- ColorSchemeCoordination - Class in etomica.graphics
-
- ColorSchemeCoordination(Simulation, PotentialMasterList, Box) - Constructor for class etomica.graphics.ColorSchemeCoordination
-
- ColorSchemeDeviation(Box, Space) - Constructor for class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- ColorSchemeDisplacement(CoordinateDefinition, Space, HSNPT.ActionSummer) - Constructor for class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- ColorSchemeDropletSurface - Class in etomica.modules.droplet
-
- ColorSchemeDropletSurface(AtomFilterCollective) - Constructor for class etomica.modules.droplet.ColorSchemeDropletSurface
-
- ColorSchemeLiquidVapor - Class in etomica.modules.droplet
-
- ColorSchemeLiquidVapor(AtomFilterCollective) - Constructor for class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- ColorSchemeNeighbor - Class in etomica.graphics
-
Color atoms based on being neighbors of the reference atom
- ColorSchemeNeighbor(PotentialMasterList, Box) - Constructor for class etomica.graphics.ColorSchemeNeighbor
-
- ColorSchemeNeighborCell - Class in etomica.graphics
-
Colors atoms based on being in a neighboring cell to a reference atom.
- ColorSchemeNeighborCell(PotentialMasterNbr, Box, int) - Constructor for class etomica.graphics.ColorSchemeNeighborCell
-
- ColorSchemeNull - Class in etomica.graphics
-
Does nothing at any time to set atom's color, leaving color to be set to default value.
- ColorSchemeNull() - Constructor for class etomica.graphics.ColorSchemeNull
-
- ColorSchemeOverlap - Class in etomica.graphics
-
Color atoms based on how many overlaps they have with their neighbors
- ColorSchemeOverlap(Space, PotentialMasterList, Box) - Constructor for class etomica.graphics.ColorSchemeOverlap
-
- colorSchemeOverlap - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- ColorSchemePlane - Class in etomica.modules.crystalviewer
-
Colors atoms according to whether or not they are in a plane,
as determined by the inPlane method of a Plane instance.
- ColorSchemePlane(LatticePlane) - Constructor for class etomica.modules.crystalviewer.ColorSchemePlane
-
- ColorSchemePlane(LatticePlane, Color, Color) - Constructor for class etomica.modules.crystalviewer.ColorSchemePlane
-
- ColorSchemeRadical - Class in etomica.modules.catalysis
-
- ColorSchemeRadical(AtomLeafAgentManager<InteractionTracker.CatalysisAgent>) - Constructor for class etomica.modules.catalysis.ColorSchemeRadical
-
- ColorSchemeRadical - Class in etomica.modules.chainequilibrium
-
- ColorSchemeRadical(AtomLeafAgentManager<IAtom[]>) - Constructor for class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- ColorSchemeRadical.LengthAgent - Class in etomica.modules.chainequilibrium
-
- ColorSchemeRandom - Class in etomica.graphics
-
- ColorSchemeRandom(Box, IRandom) - Constructor for class etomica.graphics.ColorSchemeRandom
-
- ColorSchemeRandomByMolecule - Class in etomica.graphics
-
- ColorSchemeRandomByMolecule(Simulation, Box, IRandom) - Constructor for class etomica.graphics.ColorSchemeRandomByMolecule
-
- colorSchemeScaled - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- ColorSchemeScaledOverlap - Class in etomica.normalmode.nptdemo
-
Color atoms based on being neighbors of the reference atom
- ColorSchemeScaledOverlap(Space, PotentialMasterList, CoordinateDefinition) - Constructor for class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- ColorSchemeSmer - Class in etomica.association
-
Color scheme for smer association.
- ColorSchemeSmer(IAssociationHelper, Box, IRandom) - Constructor for class etomica.association.ColorSchemeSmer
-
- ColorSchemeSmer.ColorAgent - Class in etomica.association
-
- ColorSchemeSmerByLength - Class in etomica.association
-
Color scheme for smer association.
- ColorSchemeSmerByLength(IAssociationHelper, IRandom) - Constructor for class etomica.association.ColorSchemeSmerByLength
-
- ColorSchemeStepWise - Class in etomica.modules.chainequilibrium
-
Color scheme for stepwise growth, based on the AtomType (alcohol vs.
- ColorSchemeStepWise(Simulation, AtomLeafAgentManager<IAtom[]>) - Constructor for class etomica.modules.chainequilibrium.ColorSchemeStepWise
-
- ColorSchemeTemperature - Class in etomica.graphics
-
Colors atoms according to their kinetic energy.
- ColorSchemeTemperature() - Constructor for class etomica.graphics.ColorSchemeTemperature
-
Constructs with default low of 200K and high of 400K.
- ColorSchemeTemperature(double, double) - Constructor for class etomica.graphics.ColorSchemeTemperature
-
- colorTriadToInt(float, float, float) - Static method in class org.jmol.util.ColorUtil
-
- ColorUtil - Class in org.jmol.util
-
- ColorUtil() - Constructor for class org.jmol.util.ColorUtil
-
- cols - Variable in class etomica.graphics.DeviceButtonGroup
-
- columnHeaders - Variable in class etomica.graphics.DisplayTable
-
- columnInfoFactories - Variable in class etomica.data.types.DataTable.DataInfoTableFactory
-
- columnNames - Variable in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- columnNames - Variable in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- columnNames - Variable in class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- com - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- com - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- com - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- com - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- com - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- com - Variable in class etomica.virial.MCMoveClusterRingScale
-
- com0 - Variable in class etomica.models.water.OrientationCalcWater3P
-
- com0 - Variable in class etomica.models.water.OrientationCalcWater4P
-
- com0 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- com0 - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
-
- com0 - Variable in class etomica.potential.P2HydrogenHinde
-
- com0 - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- com0 - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- com0 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- com0 - Variable in class etomica.potential.P2HydrogenPatkowski
-
- com0 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- com0 - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- com0 - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- com1 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- com1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- com1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- com1 - Variable in class etomica.models.water.P2Water4P
-
- com1 - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
-
- com1 - Variable in class etomica.potential.P2HydrogenHinde
-
- com1 - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- com1 - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- com1 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- com1 - Variable in class etomica.potential.P2HydrogenPatkowski
-
- com1 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- com2 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- com2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- com2 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- com2 - Variable in class etomica.models.water.P2Water4P
-
- com3 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- CombinationIterator - Class in etomica.math.discrete
-
Iterator that returns different combinations of n integers taken k at a time.
- CombinationIterator(int, int) - Constructor for class etomica.math.discrete.CombinationIterator
-
Constructor for CombinationIterator.
- combinationProbability - Variable in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
- combineAB - Variable in class etomica.graph.operations.MaxIsomorphWertheim
-
- CombineABSite - Class in etomica.graph.operations
-
Operation that attempts to change bonds in a graph so that equivalent graphs
in a set can be combined.
- CombineABSite() - Constructor for class etomica.graph.operations.CombineABSite
-
- CombineABSite.CombineABSiteParameters - Class in etomica.graph.operations
-
- CombineABSiteParameters(List<Character>, List<Character>) - Constructor for class etomica.graph.operations.CombineABSite.CombineABSiteParameters
-
- combineGraphs(Graph, Graph) - Method in class etomica.graph.iterators.CartesianIterator
-
- combineGraphs(Graph, Graph) - Method in class etomica.graph.iterators.PartitionedIterator
-
- combineLonelyNodes - Variable in class etomica.graph.operations.BiComponentSubst.BiComponentSubstParameters
-
- combinePermutations(byte[], byte[]) - Method in class etomica.graph.iterators.CartesianPermutator
-
- comHack - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- comHackDist - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- COMMAND_CLEAR - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_DISPLAY - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_DROP - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_LIST - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_PRINT - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_QUIT - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_READ - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_READDB - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_RUN - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_SAVE - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_SET - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_SUMMARY - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_WRITE - Static variable in interface etomica.graph.engine.Parser
-
- COMMAND_WRITEDB - Static variable in interface etomica.graph.engine.Parser
-
- CommandImpl - Class in etomica.graph.engine.impl
-
- CommandImpl(String) - Constructor for class etomica.graph.engine.impl.CommandImpl
-
- CommandPropertyValueImpl - Class in etomica.graph.engine.impl
-
- CommandPropertyValueImpl(String, Parser.Property, Parser.Value) - Constructor for class etomica.graph.engine.impl.CommandPropertyValueImpl
-
- CommandValueImpl - Class in etomica.graph.engine.impl
-
- CommandValueImpl(String, Parser.Value) - Constructor for class etomica.graph.engine.impl.CommandValueImpl
-
- CommandVariableImpl - Class in etomica.graph.engine.impl
-
- CommandVariableImpl(String, Parser.Variable) - Constructor for class etomica.graph.engine.impl.CommandVariableImpl
-
- CommandVariableValueImpl - Class in etomica.graph.engine.impl
-
- CommandVariableValueImpl(String, Parser.Variable, Parser.Value) - Constructor for class etomica.graph.engine.impl.CommandVariableValueImpl
-
- Common - Class in etomica.meta
-
- Common() - Constructor for class etomica.meta.Common
-
- comOld - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- comOld - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- comparableInstance(Bitmap) - Method in interface etomica.graph.model.Bitmap
-
Returns a bitmap instance with the same number of bits as this bitmap.
- comparableInstance(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- comparator - Variable in class etomica.graph.model.GraphList
-
- comparator - Variable in class etomica.graph.property.FFTDecomposition
-
- comparator - Variable in class etomica.virial.MeterVirialExternalFieldOverlapConfined
-
- ComparatorBiConnected - Class in etomica.graph.model.comparators
-
- ComparatorBiConnected() - Constructor for class etomica.graph.model.comparators.ComparatorBiConnected
-
- ComparatorChain - Class in etomica.graph.model.comparators
-
Comparator class that can chain together a list of comparators.
- ComparatorChain() - Constructor for class etomica.graph.model.comparators.ComparatorChain
-
- comparatorDirections - Variable in class etomica.graph.model.comparators.ComparatorChain
-
- ComparatorNodeColors - Class in etomica.graph.model.comparators
-
Compares based on graph factors (when available) or node colors.
- ComparatorNodeColors() - Constructor for class etomica.graph.model.comparators.ComparatorNodeColors
-
- ComparatorNodeColors(char[]) - Constructor for class etomica.graph.model.comparators.ComparatorNodeColors
-
- ComparatorNumEdges - Class in etomica.graph.model.comparators
-
- ComparatorNumEdges() - Constructor for class etomica.graph.model.comparators.ComparatorNumEdges
-
- ComparatorNumFieldNodes - Class in etomica.graph.model.comparators
-
- ComparatorNumFieldNodes() - Constructor for class etomica.graph.model.comparators.ComparatorNumFieldNodes
-
- ComparatorNumFieldNodesExchange() - Constructor for class etomica.virial.cluster.VirialDiagrams.ComparatorNumFieldNodesExchange
-
- ComparatorNumFieldNodesExchange() - Constructor for class etomica.virial.cluster.VirialDiagramsPT.ComparatorNumFieldNodesExchange
-
- ComparatorNumNodes - Class in etomica.graph.model.comparators
-
- ComparatorNumNodes() - Constructor for class etomica.graph.model.comparators.ComparatorNumNodes
-
- ComparatorNumRootNodes - Class in etomica.graph.model.comparators
-
- ComparatorNumRootNodes() - Constructor for class etomica.graph.model.comparators.ComparatorNumRootNodes
-
- comparators - Variable in class etomica.graph.model.comparators.ComparatorChain
-
- ComparatorStrand() - Constructor for class etomica.graph.property.FFTDecomposition.ComparatorStrand
-
- compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorBiConnected
-
- compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorChain
-
- compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorNodeColors
-
- compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorNumEdges
-
- compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorNumFieldNodes
-
- compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorNumNodes
-
- compare(Graph, Graph) - Method in class etomica.graph.model.comparators.ComparatorNumRootNodes
-
- compare(Object, Object) - Method in class etomica.graph.property.FFTDecomposition.ComparatorStrand
-
- compare(Graph, Graph) - Method in class etomica.virial.cluster.VirialDiagrams.ComparatorNumFieldNodesExchange
-
- compare(Graph, Graph) - Method in class etomica.virial.cluster.VirialDiagramsPT.ComparatorNumFieldNodesExchange
-
- compare(DoubleRange, DoubleRange) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined.RangeComparator
-
- compare(ScriptVariable, ScriptVariable) - Method in class org.jmol.script.ScriptVariable.Sort
-
- compare(Object[], Object[]) - Method in class org.jmol.util.Eigen.EigenSort
-
- comparedWV - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- comparedWV - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- comparedWV - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- comparedWV - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- comparedWV - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- comparedWV - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- comparedWV - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
-
- compareTo(Feature) - Method in class etomica.compatibility.Feature
-
- compareTo(int, Feature) - Method in class etomica.compatibility.Feature
-
- compareTo(Feature) - Method in class etomica.compatibility.NumericFeature
-
- compareTo(int, Feature) - Method in class etomica.compatibility.NumericFeature
-
- compareTo(Feature) - Method in class etomica.compatibility.StringFeature
-
- compareTo(int, Feature) - Method in class etomica.compatibility.StringFeature
-
- compareTo(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- compareTo(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong
-
- compareTo(Edge) - Method in class etomica.graph.model.impl.EdgeImpl
-
- compareTo(Graph) - Method in class etomica.graph.model.impl.GraphImpl
-
- compareTo(Metadata) - Method in class etomica.graph.model.impl.MetadataImpl
-
- compareTo(Node) - Method in class etomica.graph.model.impl.NodeImpl
-
- compareTo(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurd
-
Compares the value of this with another constant.
- compareTo(BigSurdVec) - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Compare algebraic value with oth.
- compareTo(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor
-
Compare value against another Ifactor
- compareTo(Rational) - Method in class etomica.veos.bigdecimal.Rational
-
Compares the value of this with another constant.
- compareTo(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
Compares the value of this with another constant.
- compareTo(IntSet) - Method in class etomica.virial.IntSet
-
- compareTo(MeterVirialExternalFieldSW.Near) - Method in class etomica.virial.MeterVirialExternalFieldSW.Near
-
- completeCommand(Map<String, Token>, boolean, boolean, String, int) - Static method in class org.jmol.script.Token
-
- completedActions - Variable in class etomica.action.activity.ActivityGroupSeries
-
- Complex - Class in etomica.math
-
Class that represents a complex number.
- Complex(double, double) - Constructor for class etomica.math.Complex
-
Constructs the complex number z = u + i*v
- component - Variable in class etomica.graphics.DeviceSlider
-
Object with property being modulated
- component - Variable in class etomica.graphics.DeviceSpinner
-
Object with property being modulated
- component - Variable in class etomica.models.co2.PNCO2GCPM
-
- component - Variable in class etomica.models.co2.PNGCPM
-
- component - Variable in class etomica.models.water.P2WaterSzalewicz
-
- component - Variable in class etomica.models.water.PNWaterGCPM
-
- component(int, int) - Method in interface etomica.space.Tensor
-
- component(int, int) - Method in class etomica.space1d.Tensor1D
-
- component(int, int) - Method in class etomica.space2d.Tensor2D
-
- component(int, int) - Method in class etomica.space3d.Tensor3D
-
- component(int, int) - Method in class etomica.spaceNd.TensorND
-
- ComponentEventControllerButton() - Constructor for class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
-
- ComponentEventMyPanel() - Constructor for class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
-
- componentHidden(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
-
- componentHidden(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
-
- ComponentIndex<T> - Class in etomica.meta
-
- ComponentIndex(Class<T>) - Constructor for class etomica.meta.ComponentIndex
-
- componentMoved(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
-
- componentMoved(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
-
- componentResized(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
-
- componentResized(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
-
- componentShown(ComponentEvent) - Method in class etomica.graphics.DeviceTrioControllerButton.ComponentEventControllerButton
-
- componentShown(ComponentEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ComponentEventMyPanel
-
- ComponentSubst - Class in etomica.graph.operations
-
This class handles the substitution g = A where g is a Graph and A is a set
of Graph.
- ComponentSubst() - Constructor for class etomica.graph.operations.ComponentSubst
-
- ComponentSubst.ComponentSubstParameters - Class in etomica.graph.operations
-
- ComponentSubstParameters(Graph, Set<Graph>, MulFlexible.MulFlexibleParameters) - Constructor for class etomica.graph.operations.ComponentSubst.ComponentSubstParameters
-
- CompoundDimension - Class in etomica.units.dimensions
-
- CompoundDimension(Dimension[], double[]) - Constructor for class etomica.units.dimensions.CompoundDimension
-
- CompoundDimension(Dimension[], double[], String) - Constructor for class etomica.units.dimensions.CompoundDimension
-
- CompoundUnit - Class in etomica.units
-
Unit formed from other units raised to specified powers.
- CompoundUnit(Unit[], double[]) - Constructor for class etomica.units.CompoundUnit
-
Constructs unit with default name and abbreviation constructed from given units and exponents
- CompoundUnit(Unit[], double[], String, String) - Constructor for class etomica.units.CompoundUnit
-
- compressibility - Variable in class etomica.virial.HypernettedChain
-
- compressibility - Variable in class etomica.virial.PercusYevick
-
- compressibility - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- compressibility - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- compressibility - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
-
- compressibility - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
-
- compute() - Method in class etomica.veos.bigdecimal.Wigner3jGUI
-
- computeA(int[], int[], double) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- computeA(int[], double[], double) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- computeA(int[], int[], double[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- computeA(int[], double[], double) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- computeAngle(Tuple3f, Tuple3f, Tuple3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Measure
-
- computeAngleABC(Tuple3f, Tuple3f, Tuple3f, boolean) - Static method in class org.jmol.util.Measure
-
- computeAPartitions(int, int) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- computeB(double[], int, double, boolean) - Static method in class etomica.virial.B3ForSphericallySymmetricU
-
- computeB(int, int, double, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnIETP2Spherical
-
- computeB(int, int, double, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnPY_1QC_Helium
-
- computeB(double[], int, int, double, boolean) - Method in class etomica.virial.HypernettedChain
-
- computeB(double[], int, int, double, boolean) - Method in class etomica.virial.PercusYevick
-
- computeB(double[], int, int, double, boolean) - Method in class etomica.virial.PercusYevick1QC
-
- computeB2QM(Potential2SoftSpherical, double) - Static method in class etomica.virial.B3ForSphericallySymmetricU
-
- computeB3NonAdd(Potential2SoftSpherical, PotentialSoft, Space, double) - Static method in class etomica.virial.B3NonAddForSphericallySymmetricU
-
- computeDstFiles(List) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Populates a vector with destination files names
computed from the names of the files in the sources vector
and the value of the dst property
- computeHelicalAxis(String, int, Point3f, Point3f, Quaternion) - Static method in class org.jmol.util.Measure
-
- computeImageParameters() - Method in class etomica.graphics.DisplayBox
-
- computeImageParameters() - Method in class etomica.graphics.DisplayPolytope
-
- computeImageParameters2(int, int) - Method in class etomica.graphics.DisplayBox
-
- computeImageParameters2(int, int) - Method in class etomica.graphics.DisplayPolytope
-
- computeOrigin(int, int, int) - Method in class etomica.graphics.DisplayPolytope
-
- computeP - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
-
- computeP - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
-
- computePartitions(int, int) - Method in class etomica.virial.ClusterSinglyConnected
-
- computePMA - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
-
- computePMA - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
-
- computeScaledSysParams(double, double, double, double) - Static method in class etomica.potential.EwaldSummation
-
- computeShiftOrigin(IAtom, Boundary) - Method in class etomica.graphics.DisplayBoxCanvas1D
-
- computeSources() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Populates a vector with the set of SVG files from the
srcDir if it is not null and with the sources (files or URLs)
if any.
- computeTorsion(Tuple3f, Tuple3f, Tuple3f, Tuple3f, boolean) - Static method in class org.jmol.util.Measure
-
- computeTranscodingHints() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Computes the set of transcoding hints to use for the operation
- computeU - Variable in class etomica.mappedvirial.MappedU.LJMDParams
-
- computeUMA - Variable in class etomica.mappedvirial.MappedU.LJMDParams
-
- comWi - Variable in class etomica.models.water.PNWaterGCPM
-
- comWj - Variable in class etomica.models.water.PNWaterGCPM
-
- concatList(ScriptVariable, ScriptVariable, boolean) - Static method in class org.jmol.script.ScriptVariable
-
- concatTokens(String[], int, int) - Static method in class org.jmol.util.Parser
-
- CondenseExchange - Class in etomica.virial.cluster
-
This operation replaces groups of points connected (internally) by
e-exchange bonds with a single point.
- CondenseExchange() - Constructor for class etomica.virial.cluster.CondenseExchange
-
- CondenseExchange.CondenseExchangeParameters - Class in etomica.virial.cluster
-
- CondenseExchangeParameters(char, char, char, char) - Constructor for class etomica.virial.cluster.CondenseExchange.CondenseExchangeParameters
-
- config - Variable in class etomica.interfacial.LJMC
-
- config - Variable in class etomica.interfacial.LJMD
-
- config - Variable in class etomica.modules.catalysis.Catalysis
-
- config - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- config - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- config - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- config - Variable in class etomica.modules.droplet.Droplet
-
- config - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- config - Variable in class etomica.modules.pistoncylinder.PistonCylinder
-
- config - Variable in class etomica.modules.sam.Sam
-
- configButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- configFile - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- configFile - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- ConfigFromFileLAMMPS - Class in etomica.freeenergy.npath
-
This reads ATOM files from LAMMPS and creates a display of one of the
configurations.
- ConfigFromFileLAMMPS() - Constructor for class etomica.freeenergy.npath.ConfigFromFileLAMMPS
-
- ConfigFromFileLAMMPS.AtomFilterDeviation - Class in etomica.freeenergy.npath
-
- ConfigFromFileLAMMPS.ColorSchemeDeviation - Class in etomica.freeenergy.npath
-
- ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam - Class in etomica.freeenergy.npath
-
- ConfigFromFileLAMMPS.ModifierConfiguration - Class in etomica.freeenergy.npath
-
- ConfigFromFileLAMMPSParam() - Constructor for class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam
-
- configIndex - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- configMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- configMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- configMonoLattice - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
-
- configOrthoLattice - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
-
- configuration - Variable in class etomica.action.SimulationRestart
-
- Configuration - Interface in etomica.config
-
General class for assignment of molecules to positions in a box.
- configuration - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- configuration - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- configuration - Variable in class etomica.modules.colloid.ColloidSim
-
- configuration - Variable in class etomica.modules.mu.Mu
-
- configuration - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- configuration - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- configuration - Static variable in class org.jmol.script.Token
-
- ConfigurationAligned - Class in etomica.spin
-
Configuration used to align all atoms in a spin system, so all
point in the same direction.
- ConfigurationAligned() - Constructor for class etomica.spin.ConfigurationAligned
-
- ConfigurationCatalysis - Class in etomica.modules.catalysis
-
Configuration for catalysis module.
- ConfigurationCatalysis(Simulation, Space, ISpecies, ISpecies, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.ConfigurationCatalysis
-
- ConfigurationCatalysis.BasisOrthorhombicHexagonal3D - Class in etomica.modules.catalysis
-
- ConfigurationCluster - Class in etomica.virial
-
- ConfigurationCluster(Space) - Constructor for class etomica.virial.ConfigurationCluster
-
- ConfigurationClusterAceticAcid - Class in etomica.virial
-
- ConfigurationClusterAceticAcid(Space, IRandom, MayerFunction) - Constructor for class etomica.virial.ConfigurationClusterAceticAcid
-
- ConfigurationClusterAceticAcid(Space, IRandom, MayerFunction, MayerFunction) - Constructor for class etomica.virial.ConfigurationClusterAceticAcid
-
- ConfigurationClusterAceticAcid(Space, IRandom, MayerFunction, MayerFunction, MayerFunction) - Constructor for class etomica.virial.ConfigurationClusterAceticAcid
-
- ConfigurationClusterChain - Class in etomica.virial
-
- ConfigurationClusterChain(Space) - Constructor for class etomica.virial.ConfigurationClusterChain
-
- ConfigurationClusterChainFourSites - Class in etomica.virial
-
- ConfigurationClusterChainFourSites(Space) - Constructor for class etomica.virial.ConfigurationClusterChainFourSites
-
- ConfigurationClusterMove - Class in etomica.virial
-
- ConfigurationClusterMove(Space, IRandom) - Constructor for class etomica.virial.ConfigurationClusterMove
-
- ConfigurationClusterMove(Space, IRandom, double) - Constructor for class etomica.virial.ConfigurationClusterMove
-
- ConfigurationClusterWertheimGCPM - Class in etomica.virial
-
- ConfigurationClusterWertheimGCPM(Space, IRandom, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
-
- ConfigurationClusterWertheimGCPM(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
-
- ConfigurationClusterWertheimGCPM(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
-
- ConfigurationClusterWertheimGCPM(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM
-
- ConfigurationClusterWertheimGCPM4Pt - Class in etomica.virial
-
- ConfigurationClusterWertheimGCPM4Pt(Space, IRandom, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- ConfigurationClusterWertheimGCPM4Pt(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- ConfigurationClusterWertheimGCPM4Pt(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- ConfigurationClusterWertheimGCPM4Pt(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- ConfigurationClusterWertheimGCPMDirectSampling - Class in etomica.virial
-
- ConfigurationClusterWertheimGCPMDirectSampling(Space, IRandom, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- ConfigurationClusterWertheimGCPMDirectSampling(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- ConfigurationClusterWertheimGCPMDirectSampling(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- ConfigurationClusterWertheimGCPMDirectSampling(Space, IRandom, PNWaterGCPMThreeSite, PNWaterGCPMThreeSite, double) - Constructor for class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- ConfigurationColloid - Class in etomica.modules.colloid
-
- ConfigurationColloid(Space, ISpecies, ISpecies, IRandom) - Constructor for class etomica.modules.colloid.ConfigurationColloid
-
- ConfigurationDroplet - Class in etomica.modules.droplet
-
- ConfigurationDroplet(IRandom, Space) - Constructor for class etomica.modules.droplet.ConfigurationDroplet
-
- ConfigurationFile - Class in etomica.config
-
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
- ConfigurationFile(String) - Constructor for class etomica.config.ConfigurationFile
-
- ConfigurationFileBinary - Class in etomica.config
-
reads configuration coordinates from a binary file and assigns them to the
leaf atoms in a box.
- ConfigurationFileBinary(String) - Constructor for class etomica.config.ConfigurationFileBinary
-
- ConfigurationFileTIP4P - Class in etomica.models.water
-
This reads from a configuration file containing only H, H and O.
- ConfigurationFileTIP4P(String, Space, boolean) - Constructor for class etomica.models.water.ConfigurationFileTIP4P
-
- ConfigurationFileXYZ - Class in etomica.zeolite
-
- ConfigurationFileXYZ(String, Space) - Constructor for class etomica.zeolite.ConfigurationFileXYZ
-
- ConfigurationLammps - Class in etomica.interfacial
-
- ConfigurationLammps(Space, String, ISpecies, ISpecies, ISpecies) - Constructor for class etomica.interfacial.ConfigurationLammps
-
- ConfigurationLattice - Class in etomica.config
-
Constructs configuration that has the molecules placed on the sites of a
lattice.
- ConfigurationLattice(SpaceLattice, Space) - Constructor for class etomica.config.ConfigurationLattice
-
Constructs class using instance of IndexIteratorRectangular as the default
index iterator.
- ConfigurationLattice(SpaceLattice, IndexIteratorSizable, Space) - Constructor for class etomica.config.ConfigurationLattice
-
Construct class that will place atoms on sites of the given lattice,
proceeding in the order resulting from iteration through the given index
iterator.
- ConfigurationLattice.MyLattice - Class in etomica.config
-
Used to store the state of a lattice.
- ConfigurationLatticeFreeRadical - Class in etomica.modules.chainequilibrium
-
Configuration that puts atoms randomly on a lattice and groups pairs of
initiator atoms together as though they are a single molecule.
- ConfigurationLatticeFreeRadical(SpaceLattice, Space, IRandom) - Constructor for class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
-
- ConfigurationLatticeRandom - Class in etomica.modules.chainequilibrium
-
Configuration that puts atoms randomly on a lattice.
- ConfigurationLatticeRandom(SpaceLattice, Space, IRandom) - Constructor for class etomica.modules.chainequilibrium.ConfigurationLatticeRandom
-
- ConfigurationLatticeSimple - Class in etomica.config
-
Constructs configuration that has the molecules placed on the sites of a
lattice.
- ConfigurationLatticeSimple(SpaceLattice, Space) - Constructor for class etomica.config.ConfigurationLatticeSimple
-
Constructs class using instance of IndexIteratorRectangular as the default
index iterator.
- ConfigurationLatticeSimple(SpaceLattice, IndexIteratorSizable, Space) - Constructor for class etomica.config.ConfigurationLatticeSimple
-
Construct class that will place atoms on sites of the given lattice,
proceeding in the order resulting from iteration through the given index
iterator.
- ConfigurationLatticeTube - Class in etomica.modules.dcvgcmd
-
Creates a configuration using a CubicLattice to specify positions.
- ConfigurationLatticeTube(BravaisLatticeCrystal, double, Space) - Constructor for class etomica.modules.dcvgcmd.ConfigurationLatticeTube
-
- ConfigurationLatticeTube(BravaisLatticeCrystal, double, IndexIteratorSizable, Space) - Constructor for class etomica.modules.dcvgcmd.ConfigurationLatticeTube
-
Constructor for ConfigurationLatticeTube.
- ConfigurationLatticeWithPlane - Class in etomica.config
-
Constructs configuration that has the molecules placed on the sites of a
lattice.
- ConfigurationLatticeWithPlane(SpaceLattice, Plane, Space) - Constructor for class etomica.config.ConfigurationLatticeWithPlane
-
Constructs class using instance of IndexIteratorRectangular as the default
index iterator.
- ConfigurationMembrane - Class in etomica.modules.rosmosis
-
- ConfigurationMembrane(Simulation, Space) - Constructor for class etomica.modules.rosmosis.ConfigurationMembrane
-
- ConfigurationMembraneWater - Class in etomica.modules.rosmosis
-
- ConfigurationMembraneWater(Simulation, Space) - Constructor for class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- ConfigurationMonoclinicLattice - Class in etomica.paracetamol
-
Constructs configuration that has the molecules placed on the sites of a
lattice.
- ConfigurationMonoclinicLattice(SpaceLattice, Space) - Constructor for class etomica.paracetamol.ConfigurationMonoclinicLattice
-
Constructs class using instance of IndexIteratorRectangular as the default
index iterator.
- ConfigurationMonoclinicLattice(SpaceLattice, IndexIteratorSizable, Space) - Constructor for class etomica.paracetamol.ConfigurationMonoclinicLattice
-
Construct class that will place atoms on sites of the given lattice,
proceeding in the order resulting from iteration through the given index
iterator.
- ConfigurationMonoclinicLattice.MyLattice - Class in etomica.paracetamol
-
Used to store the state of a lattice.
- ConfigurationOrientedFile - Class in etomica.config
-
ConfigurationFile subclass capable of handling oriented atoms.
- ConfigurationOrientedFile(String, Space) - Constructor for class etomica.config.ConfigurationOrientedFile
-
- ConfigurationOrthorhombicLattice - Class in etomica.paracetamol
-
Constructs configuration that has the molecules placed on the sites of a
lattice.
- ConfigurationOrthorhombicLattice(SpaceLattice, Space) - Constructor for class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
Constructs class using instance of IndexIteratorRectangular as the default
index iterator.
- ConfigurationOrthorhombicLattice(SpaceLattice, IndexIteratorSizable, Space) - Constructor for class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
Construct class that will place atoms on sites of the given lattice,
proceeding in the order resulting from iteration through the given index
iterator.
- ConfigurationOrthorhombicLattice.MyLattice - Class in etomica.paracetamol
-
Used to store the state of a lattice.
- ConfigurationOverlapException - Exception in etomica.exception
-
Exception thrown when an overlap is detected in the configuration of
a box, subject to the status of an ignoreOverlap flag.
- ConfigurationOverlapException(Box) - Constructor for exception etomica.exception.ConfigurationOverlapException
-
Constructor for ConfigurationOverlapException
- ConfigurationReplicate - Class in etomica.config
-
- ConfigurationReplicate() - Constructor for class etomica.config.ConfigurationReplicate
-
- ConfigurationResourceFile - Class in etomica.config
-
- ConfigurationResourceFile(String, Class) - Constructor for class etomica.config.ConfigurationResourceFile
-
- ConfigurationSAM - Class in etomica.modules.sam
-
- ConfigurationSAM(Simulation, Space, ISpecies, ISpecies, PotentialMasterList) - Constructor for class etomica.modules.sam.ConfigurationSAM
-
- ConfigurationUpdate - Class in etomica.server.representations
-
- ConfigurationUpdate(double[][][], Boundary[]) - Constructor for class etomica.server.representations.ConfigurationUpdate
-
- ConfigurationUpdateEncoder() - Constructor for class etomica.server.resources.ConfigurationWebsocket.ConfigurationUpdateEncoder
-
- ConfigurationWater108 - Class in etomica.rotation
-
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
- ConfigurationWater108() - Constructor for class etomica.rotation.ConfigurationWater108
-
- ConfigurationWater108TIP4P - Class in etomica.rotation
-
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
- ConfigurationWater108TIP4P() - Constructor for class etomica.rotation.ConfigurationWater108TIP4P
-
- ConfigurationWater256 - Class in etomica.rotation
-
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
- ConfigurationWater256() - Constructor for class etomica.rotation.ConfigurationWater256
-
- ConfigurationWater3 - Class in etomica.rotation
-
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
- ConfigurationWater3() - Constructor for class etomica.rotation.ConfigurationWater3
-
- ConfigurationWater3_3P - Class in etomica.rotation
-
reads configuration coordinates from a file and assigns them to the leaf atoms in a box
- ConfigurationWater3_3P() - Constructor for class etomica.rotation.ConfigurationWater3_3P
-
- ConfigurationWebsocket - Class in etomica.server.resources
-
- ConfigurationWebsocket(SimulationStore, ObjectMapper, ScheduledThreadPoolExecutor) - Constructor for class etomica.server.resources.ConfigurationWebsocket
-
- ConfigurationWebsocket.ConfigurationUpdateEncoder - Class in etomica.server.resources
-
- ConfigurationZero - Class in etomica.modules.entropylottery
-
Configuration that simply puts all the Atoms at 0, or -0.5 if the box size
is even (which makes the entropy lottery binning happy).
- ConfigurationZero(Space) - Constructor for class etomica.modules.entropylottery.ConfigurationZero
-
- ConfigurationZincblende - Class in etomica.config
-
Sets the configuration to the zincblende structure, which consists
of two fcc lattices, with one shifted in each direction by one-quarter
of the lattice constant.
- ConfigurationZincblende(double, Space) - Constructor for class etomica.config.ConfigurationZincblende
-
- confluentHypergeometric1F1(double, double, double) - Static method in class etomica.math.SpecialFunctions
-
The confluent hypergeometric function, usually given the symbol 1F1.
- confName - Variable in class etomica.action.WriteConfiguration
-
- confName - Variable in class etomica.config.ConfigurationFile
-
- confName - Variable in class etomica.config.ConfigurationFileBinary
-
- conformation - Variable in class etomica.chem.models.ModelChain
-
- conformation - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- conformation - Variable in class etomica.modules.rheology.SimulationRheology
-
- conformation - Variable in class etomica.modules.sam.ConfigurationSAM
-
- conformation - Variable in class etomica.species.Species
-
- conformation - Variable in class etomica.virial.SpeciesFactoryWater4P
-
- Conformation7SiteRigidSF6 - Class in etomica.virial
-
Conformation of SF6
7 LJ sites, rigid, no charge
Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study
- Conformation7SiteRigidSF6(Space) - Constructor for class etomica.virial.Conformation7SiteRigidSF6
-
- ConformationAceticAcid - Class in etomica.models.OPLS
-
Conformation for acetic acid
- ConformationAceticAcid(Space) - Constructor for class etomica.models.OPLS.ConformationAceticAcid
-
- ConformationAlkaneEH - Class in etomica.AlkaneEH
-
Conformation for normal alkanes, explicit hydrogen
Siepmann, TraPPE-EH
- ConformationAlkaneEH(Space, SpeciesAlkaneEH) - Constructor for class etomica.AlkaneEH.ConformationAlkaneEH
-
- ConformationAnthracene3site - Class in etomica.virial
-
Conformation for Anthracene
Reference paper: Iwai
3 site linear, group H to the two side benzene rings
- ConformationAnthracene3site(Space) - Constructor for class etomica.virial.ConformationAnthracene3site
-
- ConformationAnthraceneTraPPE - Class in etomica.virial
-
Conformation for Anthracene
Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al
modified from naphthalene conformation
- ConformationAnthraceneTraPPE(Space) - Constructor for class etomica.virial.ConformationAnthraceneTraPPE
-
- ConformationChain - Class in etomica.config
-
General class for a collection of linearly linked atoms.
- ConformationChain(Space) - Constructor for class etomica.config.ConformationChain
-
- ConformationChain2D - Class in etomica.config
-
- ConformationChain2D(Space, Vector[]) - Constructor for class etomica.config.ConformationChain2D
-
- ConformationChain3D - Class in etomica.config
-
- ConformationChain3D(Space, Vector[]) - Constructor for class etomica.config.ConformationChain3D
-
- ConformationChainLinear - Class in etomica.config
-
Places atoms in a straight line.
- ConformationChainLinear(Space) - Constructor for class etomica.config.ConformationChainLinear
-
- ConformationChainLinear(Space, double) - Constructor for class etomica.config.ConformationChainLinear
-
- ConformationChainLinear(Space, double, double[]) - Constructor for class etomica.config.ConformationChainLinear
-
- ConformationChainZigZag - Class in etomica.config
-
Takes two vectors, and returns them in repeating order to form a zig-zag chain
molecule.
- ConformationChainZigZag(Space) - Constructor for class etomica.config.ConformationChainZigZag
-
- ConformationChainZigZag(Space, Vector, Vector) - Constructor for class etomica.config.ConformationChainZigZag
-
- ConformationChainZigZag2 - Class in etomica.config
-
- ConformationChainZigZag2(Space) - Constructor for class etomica.config.ConformationChainZigZag2
-
- ConformationChainZigZag2(Space, Vector, Vector) - Constructor for class etomica.config.ConformationChainZigZag2
-
- ConformationCO2 - Class in etomica.virial
-
Conformation for CO2
Reference paper: Partial molar ~~, Stubbs Darke-Wilhelm, Siepmann, JCP
- ConformationCO2(Space) - Constructor for class etomica.virial.ConformationCO2
-
- ConformationEthanol - Class in etomica.models.rowley
-
Conformation for ethanol (positioned in standard orientation) as published in Rowley et al (2006)
K.R.
- ConformationEthanol(Space, boolean) - Constructor for class etomica.models.rowley.ConformationEthanol
-
- ConformationGeneric - Class in etomica.config
-
- ConformationGeneric(Vector[]) - Constructor for class etomica.config.ConformationGeneric
-
- ConformationHexane - Class in etomica.models.hexane
-
Defines the vectors used to create a hexane molecule according to Dr.
- ConformationHexane(Space) - Constructor for class etomica.models.hexane.ConformationHexane
-
- ConformationHSDimer - Class in etomica.normalmode
-
Conformation for HS Dimer
- ConformationHSDimer(Space, double) - Constructor for class etomica.normalmode.ConformationHSDimer
-
- ConformationLinear - Class in etomica.config
-
Places atoms in a straight line.
- ConformationLinear(Space) - Constructor for class etomica.config.ConformationLinear
-
- ConformationLinear(Space, double) - Constructor for class etomica.config.ConformationLinear
-
- ConformationLinear(Space, double, double[]) - Constructor for class etomica.config.ConformationLinear
-
- ConformationMethane - Class in etomica.AlkaneEH
-
Conformation for TraPPE-Explicit hydrogen methane
C site and H site, NOTE the H is located in the middle of C-H bond
- ConformationMethane(Space) - Constructor for class etomica.AlkaneEH.ConformationMethane
-
- ConformationMethane - Class in etomica.virial
-
Conformation for TraPPE-Explicit hydrogen methane
C site and H site, NOTE the H is located in the middle of C-H bond
- ConformationMethane(Space) - Constructor for class etomica.virial.ConformationMethane
-
- ConformationMethanol - Class in etomica.models.rowley
-
Conformation for methanol in standard orientation as published in Rowley et al (2006)
OpenOffice Spreadsheet file, Methanol coordinates, used to calculate coordinates from bond lengths and angles:
K.R.
- ConformationMethanol(Space, boolean) - Constructor for class etomica.models.rowley.ConformationMethanol
-
- ConformationMethanol - Class in etomica.models.traPPE
-
Conformation for TraPPE model of methanol: http://www.chem.umn.edu/groups/siepmann/trappe/molname.php#
CH3 group of methanol is united into a single site
K.R.
- ConformationMethanol(Space) - Constructor for class etomica.models.traPPE.ConformationMethanol
-
- ConformationNaphthaleneTraPPE - Class in etomica.virial
-
Conformation for Naphthalene
Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al
- ConformationNaphthaleneTraPPE(Space) - Constructor for class etomica.virial.ConformationNaphthaleneTraPPE
-
- ConformationNitrogen - Class in etomica.models.nitrogen
-
Conformation for Nitrogen
Reference paper: Etters RD.
- ConformationNitrogen(Space) - Constructor for class etomica.models.nitrogen.ConformationNitrogen
-
- ConformationNitrogenShellModel - Class in etomica.models.nitrogen
-
Conformation for Nitrogen (Shell Model)
Reference: Fabianski R.
- ConformationNitrogenShellModel(Space) - Constructor for class etomica.models.nitrogen.ConformationNitrogenShellModel
-
- ConformationParacetamol - Class in etomica.paracetamol
-
- ConformationParacetamol(Space) - Constructor for class etomica.paracetamol.ConformationParacetamol
-
- ConformationParacetamolMonoclinic - Class in etomica.paracetamol
-
- ConformationParacetamolMonoclinic(Space) - Constructor for class etomica.paracetamol.ConformationParacetamolMonoclinic
-
- ConformationParacetamolOrthorhombic - Class in etomica.paracetamol
-
- ConformationParacetamolOrthorhombic(Space) - Constructor for class etomica.paracetamol.ConformationParacetamolOrthorhombic
-
- ConformationPh3site - Class in etomica.virial
-
Conformation for Phenanthrene
Reference paper: Iwai
3 site group H to the two side benzene rings , eihter 464 or 545 model
modified from ConformationAnthracene
- ConformationPh3site(Space) - Constructor for class etomica.virial.ConformationPh3site
-
- ConformationPhenanthreneTraPPE - Class in etomica.virial
-
Conformation for Phenanthrene
Reference paper: TraPPE: 4 UA description of linear and branched alkanes and alkylbenzenes, Siepmann et al
modified from naphthalene
kept the axis and coorinated unchanged
- ConformationPhenanthreneTraPPE(Space) - Constructor for class etomica.virial.ConformationPhenanthreneTraPPE
-
- ConformationPolymer - Class in etomica.modules.rheology
-
Places polymer in a blob near the origin.
- ConformationPolymer(Space, IRandom) - Constructor for class etomica.modules.rheology.ConformationPolymer
-
- ConformationTube - Class in etomica.modules.dcvgcmd
-
- ConformationTube(Space, int) - Constructor for class etomica.modules.dcvgcmd.ConformationTube
-
- ConformationWater - Class in etomica.config
-
- ConformationWater(Space) - Constructor for class etomica.config.ConformationWater
-
- ConformationWater3P - Class in etomica.models.water
-
Conformation for 3-point water molecule.
- ConformationWater3P(Space) - Constructor for class etomica.models.water.ConformationWater3P
-
- ConformationWaterGCPM - Class in etomica.models.water
-
- ConformationWaterGCPM(Space) - Constructor for class etomica.models.water.ConformationWaterGCPM
-
- ConformationWaterGCPMCOM - Class in etomica.models.water
-
Conformation for 4-point water molecule (plus 1 site at the COM).
- ConformationWaterGCPMCOM(Space) - Constructor for class etomica.models.water.ConformationWaterGCPMCOM
-
- ConformationWaterTIP4P - Class in etomica.models.water
-
Conformation for 4-point water molecule.
- ConformationWaterTIP4P(Space) - Constructor for class etomica.models.water.ConformationWaterTIP4P
-
- conjugate() - Method in class etomica.math.Complex
-
Complex conjugate of this Complex number
(the conjugate of x+i*y is x-i*y).
- conjugate() - Method in class etomica.math.Quaternion
-
Returns the complex conjugate of the Quaternion q.
- ConjugateGradients - Class in etomica.conjugategradient
-
- ConjugateGradients(Matrix, Matrix, Matrix, int) - Constructor for class etomica.conjugategradient.ConjugateGradients
-
- ConjugateGradientsAlgorithm() - Method in class etomica.conjugategradient.ConjugateGradients
-
Conjugate Gradients solution for
Ax = b
- connect - Static variable in class org.jmol.script.Token
-
- connected - Static variable in class org.jmol.script.Token
-
- ConnectedToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.ConnectedToggler
-
- Console - Interface in etomica.graph.engine
-
- ConsoleContainer - Interface in etomica.graph.engine
-
- ConsoleReader - Interface in etomica.graph.engine
-
- ConsoleUI - Class in etomica.graph.engine
-
- ConsoleUI() - Constructor for class etomica.graph.engine.ConsoleUI
-
- ConsoleWindow(ConsoleUI) - Constructor for class etomica.graph.engine.Launcher.ConsoleWindow
-
- ConsoleWindowRunnable(Launcher.ConsoleWindow) - Constructor for class etomica.graph.engine.Launcher.ConsoleWindowRunnable
-
- Constant() - Constructor for class etomica.math.function.Function.Constant
-
- Constant(double) - Constructor for class etomica.math.function.Function.Constant
-
- Constants - Class in etomica.util
-
Collection of assorted physical constants.
- Constants.CompassDirection - Enum in etomica.util
-
Enumerated type for the compass directions NORTH, SOUTH, EAST, WEST.
- constMu - Variable in class etomica.modules.ensembles.LJMCGraphic
-
- constMu - Variable in class etomica.modules.statistics.StatisticsMCGraphic
-
- constrainScriptOrigin - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Controls whether scripts can only have the same origin as
the document which references them.
- constraint - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- constraint - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- constraint - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- constraint - Variable in class etomica.normalmode.P1ConstraintNbr
-
- constraintAngle - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- constraintAngle - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- constraintAngle - Variable in class etomica.models.nitrogen.MeterDirectInitPert
-
- constraintAngle - Variable in class etomica.models.nitrogen.PRotConstraint
-
- constraintAngle - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- constraintEnergy(Box) - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
Returns true if all atoms in the given box satisfy p1's constraint
- constraintEnergy(Box) - Method in class etomica.normalmode.MeterDDP
-
Returns true if all atoms in the given box satisfy p1's constraint
- constraintEnergy(Box) - Method in class etomica.normalmode.MeterDP
-
Returns true if all atoms in the given box satisfy p1's constraint
- constraintEnergy(Box) - Method in class etomica.normalmode.MeterTargetTP
-
Returns true if all atoms in the given box satisfy p1's constraint
- constraintMap - Variable in class etomica.virial.MCMoveClusterMoleculeMulti
-
- constraintMap - Variable in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- constraintPotential - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- constructHessianMatrix(String, int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- constructHessianMatrix(String, int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- constructHessianMatrix(String, int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- constructHessianMatrix(String, int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- constructHessianMatrix(int) - Method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- Construction - Class in etomica.server.core.construction
-
- Construction() - Constructor for class etomica.server.core.construction.Construction
-
- ConstructionInfo - Class in etomica.server.representations
-
- ConstructionInfo(String, List<String>, Map<String, List<Long>>, Map<String, String>) - Constructor for class etomica.server.representations.ConstructionInfo
-
- ConstructionParams - Class in etomica.server.representations
-
- ConstructionParams() - Constructor for class etomica.server.representations.ConstructionParams
-
- CONSTRUCTOR_COLORED - Static variable in interface etomica.graph.engine.Parser
-
- CONSTRUCTOR_ISOCOLORED - Static variable in interface etomica.graph.engine.Parser
-
- CONSTRUCTOR_ISOMONO - Static variable in interface etomica.graph.engine.Parser
-
- CONSTRUCTOR_MONO - Static variable in interface etomica.graph.engine.Parser
-
- ConstructorColoredImpl - Class in etomica.graph.engine.impl
-
- ConstructorColoredImpl(Map<Character, Byte>, Map<Character, Byte>, boolean) - Constructor for class etomica.graph.engine.impl.ConstructorColoredImpl
-
- ConstructorImpl - Class in etomica.graph.engine.impl
-
- ConstructorImpl() - Constructor for class etomica.graph.engine.impl.ConstructorImpl
-
- ConstructorMonoImpl - Class in etomica.graph.engine.impl
-
- ConstructorMonoImpl(byte, byte, boolean) - Constructor for class etomica.graph.engine.impl.ConstructorMonoImpl
-
- constructorParams - Variable in class etomica.server.representations.ConstructionParams
-
- constructorParams - Variable in class etomica.server.representations.SimulationConstructor
-
- cont - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- contact - Static variable in class org.jmol.script.Token
-
- contains(IAtom) - Method in class etomica.atom.AtomArrayList
-
Returns true if the given atom is in the list, false otherwise
- CONTAINS - Static variable in class etomica.compatibility.Feature
-
- contains(Object) - Method in class etomica.graph.model.GraphList
-
- contains(double) - Method in class etomica.math.DoubleRange
-
Indicates if a value falls within the range of this instance.
- contains(Vector) - Method in class etomica.math.geometry.Cube
-
Returns true if the given vector lies inside (or on the surface of)
this cell, false otherwise.
- contains(Vector) - Method in class etomica.math.geometry.Cuboid
-
Returns true if the given vector lies inside (or on the
surface of) this cell, false otherwise.
- contains(Vector) - Method in class etomica.math.geometry.Hypersphere
-
Returns true if the given point lies on or in the sphere.
- contains(Vector) - Method in class etomica.math.geometry.LineSegment
-
Returns true if the given vector lies between the ends of the segment, on
the line joining them.
- contains(Vector) - Method in class etomica.math.geometry.Parallelepiped
-
Returns true if the given vector lies inside (or on the
surface of) this cell, false otherwise.
- contains(Vector) - Method in class etomica.math.geometry.Parallelogram
-
Returns true if the given vector lies inside (or on the
surface of) this cell, false otherwise.
- contains(Vector) - Method in class etomica.math.geometry.Point
-
Returns true if this point is at exactly the same location as the point
defined by the given vector.
- contains(Vector) - Method in class etomica.math.geometry.PolygonGeneral
-
Returns true if the given point lies inside or on an edge of the polygon
- contains(Vector) - Method in class etomica.math.geometry.PolyhedronGeneral
-
Returns true if the given point lies inside or on an edge of the polyhedron
- contains(Vector) - Method in class etomica.math.geometry.Polytope
-
Returns true if the given vector lies inside the polytope,
false otherwise.
- contains(Vector) - Method in class etomica.math.geometry.Rectangle
-
Returns true if the given vector lies inside (or on the surface of)
this cell, false otherwise.
- contains(Vector) - Method in interface etomica.math.geometry.Shape
-
Returns true if the point described by the vector lies in or on the
enclosed region.
- contains(Vector) - Method in class etomica.math.geometry.Square
-
Returns true if the given vector lies inside (or on the surface of)
this cell, false otherwise.
- contains(Vector) - Method in class etomica.math.geometry.TruncatedOctahedron
-
- contains(IAtom) - Method in class etomica.potential.P2HardBondedList.BondArrayList
-
- contains(IPotentialAtomic) - Method in class etomica.potential.PotentialGroup
-
Indicates if a given potential is a sub-potential of this group.
- contains(BigInteger) - Method in class etomica.veos.bigdecimal.Prime
-
Test if a number is a prime.
- containsAll(Collection<?>) - Method in class etomica.graph.model.GraphList
-
- containsKey(Object) - Method in class etomica.util.collections.IndexMap
-
- containsKey(int) - Method in class etomica.util.collections.IndexMap
-
- containsValue(Object) - Method in class etomica.util.collections.IndexMap
-
- continuous - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- continuous - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- contourlines - Static variable in class org.jmol.script.Token
-
- controlGraphic() - Method in class etomica.graphics.DevicePlotPoints
-
Returns the top level panel that the points table and (if parameters are
vertically-oriented) function parameter slider components sit on.
- Controller - Class in etomica.action.activity
-
Organizer and executor of actions performed by the simulation.
- Controller() - Constructor for class etomica.action.activity.Controller
-
- controller - Variable in class etomica.action.activity.ControllerEvent
-
- controller - Variable in class etomica.action.ControllerActionAdapter
-
- controller - Variable in class etomica.AlkaneEH.CH4NVT
-
- controller - Variable in class etomica.AlkaneEH.DHS_NVT
-
- controller - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
-
- controller - Variable in class etomica.densityofstate.DensityOfState
-
- controller - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
-
- controller - Variable in class etomica.dielectric.DHS_NVT
-
- controller - Variable in class etomica.dielectric.DLJ_NVT_1site
-
- controller - Variable in class etomica.dielectric.TIP4P_NVT
-
- controller - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- controller - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- controller - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Controls some aspects of the converter's operation,
such as whether or not it should proceed in some
error situations.
- controller - Variable in class etomica.graphics.Device
-
- controller - Variable in class etomica.graphics.DisplayBox
-
- controller - Variable in class etomica.graphics.DisplayCanvas
-
- controller - Variable in class etomica.graphics.SimulationGraphic
-
- controller - Variable in class etomica.meam.EFSTungsten
-
- controller - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- controller - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- controller - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- controller - Variable in class etomica.meam.MEAM_MC
-
- controller - Variable in class etomica.meam.MEAMMd3D
-
- controller - Variable in class etomica.normalmode.SimOverlapModule
-
- controller - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- controller - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- controller - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- controller - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- controller - Variable in class etomica.simulation.prototypes.HSMC2D
-
- controller - Variable in class etomica.simulation.prototypes.LJMD2D
-
- controller - Variable in class etomica.simulation.prototypes.LJMD3D
-
- controller - Variable in class etomica.simulation.prototypes.SWMD2D
-
- controller - Variable in class etomica.simulation.prototypes.SWMD3D
-
- controller - Variable in class etomica.tests.TestLJGCMC3D
-
- controller - Variable in class etomica.tests.TestLJMC3D
-
- controller - Variable in class etomica.thermointegration.LjMc3D
-
- controller - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- controller - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- controller - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- controller - Variable in class etomica.yukawa.TestHC2YukawaMC3D
-
- controller - Variable in class etomica.yukawa.TestYukawaMC3D
-
- Controller.ActionStatus - Enum in etomica.action.activity
-
Enumerated type describing the status of an action.
- Controller.WaitObject - Class in etomica.action.activity
-
- controller1 - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- controller1 - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- controller1 - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- ControllerAction - Interface in etomica.action
-
Elementary action performed on a controller.
- ControllerActionAdapter - Class in etomica.action
-
Convenience class used to define a ControllerAction.
- ControllerActionAdapter() - Constructor for class etomica.action.ControllerActionAdapter
-
- ControllerAlertMsgBox - Class in etomica.virial.GUI.controllers
-
- ControllerAlertMsgBox(String, ModelSpeciesSelection) - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBox
-
- ControllerAlertMsgBox.CloseWindowButtonListener - Class in etomica.virial.GUI.controllers
-
- ControllerAlertMsgBoxSpeciesRemoval - Class in etomica.virial.GUI.controllers
-
- ControllerAlertMsgBoxSpeciesRemoval(String, ModelSpeciesSelection, int) - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval
-
- ControllerAlertMsgBoxSpeciesRemoval.NoDoNotRemoveSpeciesButtonListener - Class in etomica.virial.GUI.controllers
-
- ControllerAlertMsgBoxSpeciesRemoval.YesRemoveSpeciesButtonListener - Class in etomica.virial.GUI.controllers
-
- ControllerAlkaneLengthSelection - Class in etomica.virial.GUI.controllers
-
- ControllerAlkaneLengthSelection(ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- ControllerEvent - Class in etomica.action.activity
-
- ControllerEvent(Controller, ControllerEvent.Type) - Constructor for class etomica.action.activity.ControllerEvent
-
- ControllerEvent(Controller, ControllerEvent.Type, IAction) - Constructor for class etomica.action.activity.ControllerEvent
-
- ControllerEvent.Type - Enum in etomica.action.activity
-
- ControllerSimEnvironmentSelection - Class in etomica.virial.GUI.controllers
-
- ControllerSimEnvironmentSelection(ModelSimulationEnvironment) - Constructor for class etomica.virial.GUI.controllers.ControllerSimEnvironmentSelection
-
- controllerSpeciesSelection - Variable in class etomica.virial.GUI.controllers.AppControllerMixtureBuilder
-
- ControllerSpeciesSelection - Class in etomica.virial.GUI.controllers
-
- ControllerToggle - Class in etomica.action
-
Switches controller between paused and unpaused conditions, or starts
it if not yet active.
- ControllerToggle() - Constructor for class etomica.action.ControllerToggle
-
- controlPanel - Variable in class etomica.graphics.SimulationPanel
-
- ControlResource - Class in etomica.server.resources
-
- ControlResource(SimulationStore) - Constructor for class etomica.server.resources.ControlResource
-
- contructFullMatrix(CoordinateDefinition, String) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- contructFullMatrix(CoordinateDefinition, String) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- Conv - Class in etomica.graph.operations
-
- Conv() - Constructor for class etomica.graph.operations.Conv
-
- Converter(String) - Static method in class etomica.zeolite.Zeolite
-
- Converter(String) - Static method in class etomica.zeolite.ZeoliteSimulation
-
- convertPointFromScreen(Object, Point3f) - Method in interface org.jmol.api.ApiPlatform
-
- convertPointFromScreen(Object, Point3f) - Method in class org.jmol.awt.Platform
-
- convolution(ClusterDiagram, ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations
-
Returns a new cluster that is a convolution of the given cluster, which is obtained by joining a root point
from each diagram and turning it into a field point.
- convolution(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Returns an array of clusters formed from taking the convolution of each of the diagrams
of the first set with each of the diagrams of the second set.
- ConvParameters - Class in etomica.graph.operations
-
- ConvParameters(byte, Mul.MulParameters) - Constructor for class etomica.graph.operations.ConvParameters
-
- coord - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedSite
-
- coord2 - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedFullSite
-
- coord3 - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedFullSite
-
- coordDef - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- coordDef - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- coordDef - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- CoordinateConverter - Class in etomica.math.geometry.coordinate
-
- CoordinateConverter() - Constructor for class etomica.math.geometry.coordinate.CoordinateConverter
-
- coordinateDef - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- coordinateDef - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- coordinateDef - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- coordinateDef - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- coordinateDef - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- coordinateDef - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- coordinateDef - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- coordinateDef - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- coordinateDef - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- coordinateDef - Variable in class etomica.models.nitrogen.MeterDirectInitPert
-
- coordinateDef - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- coordinateDef - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- coordinateDef - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- coordinateDef - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- coordinateDef - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- coordinateDef - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- coordinateDef - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- coordinateDef - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- coordinateDef - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- coordinateDef - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- coordinateDef - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- coordinateDef - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- coordinateDef - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- coordinateDefinition - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
-
- coordinateDefinition - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- coordinateDefinition - Variable in class etomica.meam.EFSTungsten
-
- coordinateDefinition - Variable in class etomica.meam.PotentialEAM_LS
-
- coordinateDefinition - Variable in class etomica.models.hexane.SimHarmonicHexane
-
- coordinateDefinition - Variable in class etomica.models.hexane.TestHexane
-
- coordinateDefinition - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- coordinateDefinition - Variable in class etomica.models.hexane.TestHexaneHarmonic
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.MeterNormalizedCoord
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.MeterNormalizedCoordBeta
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.MeterOrientationDistribution
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.MeterOrientationOrderParameter
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.MeterRotationDistributionGroup
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- coordinateDefinition - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- coordinateDefinition - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- coordinateDefinition - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- coordinateDefinition - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- coordinateDefinition - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
-
- coordinateDefinition - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
-
- coordinateDefinition - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
-
- coordinateDefinition - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
-
- coordinateDefinition - Variable in class etomica.models.oneDHardRods.SimWidomMode
-
- coordinateDefinition - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- coordinateDefinition - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- coordinateDefinition - Variable in class etomica.normalmode.CalcJacobian
-
- CoordinateDefinition - Class in etomica.normalmode
-
An abstract class that defines the real-space generalized coordinates that are
summed (over molecules) to form collective coordinates (from which normal
coordinates are determined).
- CoordinateDefinition(Box, int, Primitive, Space) - Constructor for class etomica.normalmode.CoordinateDefinition
-
- CoordinateDefinition(Box, int, Primitive, Basis, Space) - Constructor for class etomica.normalmode.CoordinateDefinition
-
- coordinateDefinition - Variable in class etomica.normalmode.HessianDB
-
- coordinateDefinition - Variable in class etomica.normalmode.HSDimerNPT
-
- coordinateDefinition - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- coordinateDefinition - Variable in class etomica.normalmode.HSNPT
-
- coordinateDefinition - Variable in class etomica.normalmode.HTTPSoftSphereSim
-
- coordinateDefinition - Variable in class etomica.normalmode.IntegratorHarmonic
-
- coordinateDefinition - Variable in class etomica.normalmode.LJVacancyMin
-
- coordinateDefinition - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- coordinateDefinition - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- coordinateDefinition - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- coordinateDefinition - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
-
- coordinateDefinition - Variable in class etomica.normalmode.MCMoveHarmonic
-
- coordinateDefinition - Variable in class etomica.normalmode.MCMoveHarmonicStep
-
- coordinateDefinition - Variable in class etomica.normalmode.MCMovePhaseAngle
-
- coordinateDefinition - Variable in class etomica.normalmode.MCMoveSingleMode
-
- coordinateDefinition - Variable in class etomica.normalmode.MCMoveVolumeSolid
-
- coordinateDefinition - Variable in class etomica.normalmode.MCMoveWV
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterAtomicDisplacement
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterDADB
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterDDP
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterDisplacementMoleculeRMS
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterDisplacementRMS
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterDP
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterHarmonicCoordinate
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterHarmonicEnergy
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterJacobian
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterNormalMode
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterSolidMirror
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterSolidProps
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- coordinateDefinition - Variable in class etomica.normalmode.MeterTargetTP
-
- coordinateDefinition - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- coordinateDefinition - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- coordinateDefinition - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- coordinateDefinition - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- coordinateDefinition - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- coordinateDefinition - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- coordinateDefinition - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- coordinateDefinition - Variable in class etomica.normalmode.SimBennet
-
- coordinateDefinition - Variable in class etomica.normalmode.SimCalcJ
-
- coordinateDefinition - Variable in class etomica.normalmode.SimCalcS
-
- coordinateDefinition - Variable in class etomica.normalmode.SimCalcSLJ
-
- coordinateDefinition - Variable in class etomica.normalmode.SimCalcSMorse
-
- coordinateDefinition - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
-
- coordinateDefinition - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- coordinateDefinition - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- coordinateDefinition - Variable in class etomica.normalmode.SimHarmonic
-
- coordinateDefinition - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- coordinateDefinition - Variable in class etomica.normalmode.SimLJHTTISuper
-
- coordinateDefinition - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- coordinateDefinition - Variable in class etomica.normalmode.SimModesJ
-
- coordinateDefinition - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- coordinateDefinition - Variable in class etomica.normalmode.SimTarget
-
- coordinateDefinition - Variable in class etomica.normalmode.SimTargetUmbrella
-
- coordinateDefinition - Variable in class etomica.normalmode.SimUmbrella
-
- coordinateDefinition - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- coordinateDefinition - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
-
- coordinateDefinition - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
-
- coordinateDefinition - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
-
- coordinateDefinition - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
-
- CoordinateDefinition.BasisCell - Class in etomica.normalmode
-
- CoordinateDefinition.SiteSource - Class in etomica.normalmode
-
- CoordinateDefinitionHexane - Class in etomica.models.hexane
-
Implementation of CoordinateDefinitionMolecule that handles hexane.
- CoordinateDefinitionHexane(Simulation, Box, Primitive, SpeciesHexane, Space) - Constructor for class etomica.models.hexane.CoordinateDefinitionHexane
-
- CoordinateDefinitionHSDimer - Class in etomica.normalmode
-
CoordinateDefinition implementation for HS Dimer.
- CoordinateDefinitionHSDimer(Simulation, Box, Primitive, Basis, Space) - Constructor for class etomica.normalmode.CoordinateDefinitionHSDimer
-
- CoordinateDefinitionHSDimer.IntegerFunction - Interface in etomica.normalmode
-
- CoordinateDefinitionLeaf - Class in etomica.normalmode
-
CoordinateDefinition implementation for monatomic molecules that are simply
leaf atoms.
- CoordinateDefinitionLeaf(Box, Primitive, Space) - Constructor for class etomica.normalmode.CoordinateDefinitionLeaf
-
- CoordinateDefinitionLeaf(Box, Primitive, Basis, Space) - Constructor for class etomica.normalmode.CoordinateDefinitionLeaf
-
- CoordinateDefinitionLeafSuperBox - Class in etomica.normalmode
-
- CoordinateDefinitionLeafSuperBox(Box, Primitive, Basis, Space) - Constructor for class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- CoordinateDefinitionMolecule - Class in etomica.normalmode
-
CoordinateDefinition implementation for molecules.
- CoordinateDefinitionMolecule(Simulation, Box, Primitive, int, Space) - Constructor for class etomica.normalmode.CoordinateDefinitionMolecule
-
- CoordinateDefinitionMolecule(Simulation, Box, Primitive, int, Basis, Space) - Constructor for class etomica.normalmode.CoordinateDefinitionMolecule
-
- CoordinateDefinitionMolecule.MoleculeSiteSource - Class in etomica.normalmode
-
- CoordinateDefinitionMoleculeVolumeFluctuation - Class in etomica.normalmode
-
CoordinateDefinition implementation for molecules.
- CoordinateDefinitionMoleculeVolumeFluctuation(Simulation, Box, Primitive, int, Space) - Constructor for class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- CoordinateDefinitionMoleculeVolumeFluctuation(Simulation, Box, Primitive, int, Basis, Space) - Constructor for class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource - Class in etomica.normalmode
-
- CoordinateDefinitionNitrogen - Class in etomica.models.nitrogen
-
CoordinateDefinition implementation for nitrogen molecule.
- CoordinateDefinitionNitrogen(Simulation, Box, Primitive, Basis, Space) - Constructor for class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- CoordinateDefinitionNitrogen(Simulation, Box, Primitive, Basis, Space, int) - Constructor for class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- CoordinateDefinitionNitrogen.OrientationAgentSource - Class in etomica.models.nitrogen
-
- CoordinateDefinitionNitrogenSuperBox - Class in etomica.models.nitrogen
-
CoordinateDefinition implementation for nitrogen molecule.
- CoordinateDefinitionNitrogenSuperBox(Simulation, Box, Primitive, Basis, Space) - Constructor for class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource - Class in etomica.models.nitrogen
-
- CoordinateDefinitionParacetamol - Class in etomica.paracetamol
-
CoordinateDefinition implementation for paracetamol molecule.
- CoordinateDefinitionParacetamol(Simulation, Box, Primitive, Basis, Space) - Constructor for class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- CoordinateDefinitionParacetamol.OrientationAgentSource - Class in etomica.paracetamol
-
- coordinateDefTarg - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
-
- coordinateDim - Variable in class etomica.normalmode.CalcJacobian
-
- coordinateDim - Variable in class etomica.normalmode.CoordinateDefinition
-
- CoordinatePairLeafSet - Class in etomica.virial
-
- CoordinatePairLeafSet(IAtomList, Space) - Constructor for class etomica.virial.CoordinatePairLeafSet
-
Constructor for CoordinatePairLeafSet.
- CoordinatePairMoleculeSet - Class in etomica.virial
-
- CoordinatePairMoleculeSet(IMoleculeList, Space) - Constructor for class etomica.virial.CoordinatePairMoleculeSet
-
Constructor for CoordinatePairLeafSet.
- CoordinatePairSet - Interface in etomica.virial
-
- coordinteDefinition - Variable in class etomica.normalmode.MeterSolidDA
-
- coordinteDefinition - Variable in class etomica.normalmode.MeterSolidDACut
-
- coords - Variable in class etomica.config.ConformationGeneric
-
- Copper - Class in etomica.chem.elements
-
Class for the Copper element.
- Copper(String) - Constructor for class etomica.chem.elements.Copper
-
- Copper(String, double) - Constructor for class etomica.chem.elements.Copper
-
- copy() - Method in interface etomica.graph.isomorphism.SearchState
-
- copy(SearchState) - Method in interface etomica.graph.isomorphism.SearchState
-
- copy() - Method in class etomica.graph.isomorphism.UllmanSearchState
-
- copy(SearchState) - Method in class etomica.graph.isomorphism.UllmanSearchState
-
- copy() - Method in class etomica.graph.isomorphism.VF2SearchState
-
- copy(SearchState) - Method in class etomica.graph.isomorphism.VF2SearchState
-
- copy() - Method in class etomica.graph.isomorphism.VFSearchState
-
- copy(SearchState) - Method in class etomica.graph.isomorphism.VFSearchState
-
- copy() - Method in interface etomica.graph.model.Bitmap
-
Creates an instance-compatible copy of this bitmap.
- copy() - Method in interface etomica.graph.model.Coefficient
-
- copy() - Method in interface etomica.graph.model.Edge
-
- copy() - Method in interface etomica.graph.model.Graph
-
- copy() - Method in class etomica.graph.model.impl.AbstractBitmap
-
- copy() - Method in class etomica.graph.model.impl.CoefficientImpl
-
- copy() - Method in class etomica.graph.model.impl.EdgeImpl
-
- copy() - Method in class etomica.graph.model.impl.GraphImpl
-
- copy() - Method in class etomica.graph.model.impl.NodeImpl
-
- copy() - Method in interface etomica.graph.model.Node
-
- copy() - Method in class etomica.lattice.crystal.Primitive
-
Returns a new, identical instance of this primitive.
- copy() - Method in class etomica.lattice.crystal.PrimitiveBcc
-
Returns a new PrimitiveCubic with the same size as this one.
- copy() - Method in class etomica.lattice.crystal.PrimitiveCubic
-
Returns a new PrimitiveCubic with the same size as this one.
- copy() - Method in class etomica.lattice.crystal.PrimitiveFcc
-
Returns a new PrimitiveCubic with the same size as this one.
- copy() - Method in class etomica.lattice.crystal.PrimitiveGeneral
-
- copy() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
Returns a new PrimitiveHexagonal with the same size as this one.
- copy() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
Returns a new PrimitiveHexagonal with the same size as this one.
- copy() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
Returns a new, identical instance of this primitive.
- copy() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
Returns a new, identical instance of this primitive.
- copy() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
Returns a new, identical instance of this primitive.
- copy() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
Returns a new PrimitiveTetragonal with the same size as this one.
- copy() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
Returns a new, identical instance of this primitive.
- copy() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
Returns a new, identical instance of this primitive.
- copy() - Method in class etomica.models.hexane.PrimitiveHexane
-
Returns a new, identical instance of this primitive.
- copy() - Method in class etomica.virial.IntSet
-
- copy(BitSet) - Static method in class org.jmol.util.BitSetUtil
-
- copy2(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
-
- copyColixTranslucency(short, short) - Static method in class org.jmol.util.Colix
-
- copyFrom(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- copyFrom(String) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- copyFrom(byte[]) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- copyFrom(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong
-
TIME = O(1).
- copyFrom(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- copyHighest(int) - Method in interface etomica.graph.model.Bitmap
-
Creates an instance-compatible copy of highest numBits bits of this bitmap.
- copyHighest(int) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- copyInvert(BitSet, int) - Static method in class org.jmol.util.BitSetUtil
-
- copyLowest(int) - Method in interface etomica.graph.model.Bitmap
-
Creates an instance-compatible copy of lowest numBits bits of this bitmap.
- copyLowest(int) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- CopyOfOrthogonalPolynomial - Class in etomica.densityofstate
-
- CopyOfOrthogonalPolynomial() - Constructor for class etomica.densityofstate.CopyOfOrthogonalPolynomial
-
- copyright - Static variable in class org.jmol.viewer.JmolConstants
-
- copyTo(ClusterDiagram) - Method in class etomica.virial.cluster.ClusterDiagram
-
- core - Static variable in class etomica.models.co2.P2CO2H2OWheatley
-
- core - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- core - Variable in class etomica.models.water.PNWaterGCPM
-
- core(BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate core(n).
- core() - Method in class etomica.veos.bigdecimal.Ifactor
-
The square-free part.
- core_1 - Variable in class etomica.graph.isomorphism.AbstractSearchState
-
- core_2 - Variable in class etomica.graph.isomorphism.AbstractSearchState
-
- core_len - Variable in class etomica.graph.isomorphism.AbstractSearchState
-
- coreCluster - Variable in class etomica.virial.ClusterSumMultibodyShell
-
- coreCluster - Variable in class etomica.virial.ClusterSumShell
-
- coreCO - Static variable in class etomica.models.co2.P2CO2H2OWheatley
-
- coreDiameter - Variable in class etomica.modules.catalysis.P2SquareWellBonding
-
- coreDiameter - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- coreDiameter - Variable in class etomica.modules.catalysis.P2SquareWellSurface
-
- coreDiameter - Variable in class etomica.modules.mu.P2SquareWellOneSide
-
- coreDiameter - Variable in class etomica.potential.P2DoubleWell
-
- coreDiameter - Variable in class etomica.potential.P2PenetrableSphere
-
- coreDiameter - Variable in class etomica.potential.P2SquareWell
-
- coreDiameter - Variable in class etomica.potential.P2SquareWellRobust
-
- coreDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellBonding
-
- coreDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- coreDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellSurface
-
- coreDiameterSquared - Variable in class etomica.modules.mu.P2SquareWellOneSide
-
- coreDiameterSquared - Variable in class etomica.potential.P2DoubleWell
-
- coreDiameterSquared - Variable in class etomica.potential.P2PenetrableSphere
-
- coreDiameterSquared - Variable in class etomica.potential.P2PenetrableSquareWell
-
- coreDiameterSquared - Variable in class etomica.potential.P2SquareWell
-
- coreDiameterSquared - Variable in class etomica.potential.P2SquareWellRobust
-
- coreFac - Variable in class etomica.models.co2.PNCO2GCPM
-
- coreFac - Variable in class etomica.models.co2.PNGCPM
-
- cornerData - Variable in class etomica.util.Grabber
-
- CornerData() - Constructor for class etomica.util.Grabber.CornerData
-
- CornerSetListener(Grabber, Grabber.ActionCornerSetter, int) - Constructor for class etomica.util.Grabber.CornerSetListener
-
- corrector() - Method in class etomica.integrator.IntegratorGear4
-
- corrector() - Method in class etomica.integrator.IntegratorGear4NPH
-
- correlationSum - Variable in class etomica.data.AccumulatorAverageCollapsing
-
- correlationSum - Variable in class etomica.data.AccumulatorAverageFixed
-
- correlationSum - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- corrugationButton - Variable in class etomica.modules.sam.SamGraphic
-
- cos() - Method in class etomica.math.Complex
-
Cosine of this Complex number (doesn't change this Complex number).
- cos(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Trigonometric cosine.
- cos1m2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- cos1m2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- cos2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- cos2ThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- cosDtheta - Variable in class etomica.dimer.IntegratorDimerMin
-
- cosg - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- cosg - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- cosGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal
-
- cosGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- cosh() - Method in class etomica.math.Complex
-
Hyperbolic cosine of this Complex number
(doesn't change this Complex number).
- cosh(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The hyperbolic cosine.
- coskrj - Variable in class etomica.potential.EwaldSummation
-
- cosNominalTheta - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- cosNTheta - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- cosNTheta - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- cosTheta - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- cosThetaConstraint - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- cosThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- cosThetaDiff - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- cosThetaSum - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- cosThetaSum - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- cot(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The trigonometric co-tangent.
- cot(double) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
trigonometric cot.
- Coulomb - Class in etomica.units
-
The Coulomb unit of electrical charge.
- count - Variable in class etomica.box.BoxMoleculeCountEvent
-
- count - Variable in class etomica.data.AccumulatorAverage
-
- count - Variable in class etomica.data.AccumulatorAverageBlockless.AllData
-
- count - Variable in class etomica.data.AccumulatorAverageBlockless
-
- count - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
-
- count - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- count - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- count - Variable in class etomica.data.histogram.HistogramNotSoSimple
-
- count - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- count - Static variable in class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D
-
- count - Variable in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- count - Variable in class etomica.normalmode.HSNPT.ActionSummer
-
- count - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- count - Variable in class etomica.normalmode.WriteS
-
- Count - Class in etomica.units
-
Unit class for the number, or quantity, of something.
- count - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- count - Static variable in class etomica.virial.MeterVirialIC
-
- count1 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- countEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheim2Site
-
- countEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheim2SiteRho
-
- countEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho
-
- counter - Variable in class etomica.atom.iterator.ANIntergroupCoupled
-
- counter - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- counter - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- counter - Variable in class etomica.dimer.IntegratorDimerMin
-
- counter - Variable in class etomica.dimer.IntegratorDimerRT
-
- counter - Variable in class etomica.models.nitrogen.PRotConstraint
-
- counter - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- counter - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
-
- counter - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- counter - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
-
- counter - Variable in class etomica.models.oneDHardRods.MeterWidomMode
-
- counter - Variable in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- counter - Variable in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- countflips - Variable in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- countMolecules(String) - Static method in class etomica.potential.PotentialEmul
-
- counts - Variable in class etomica.data.histogram.HistogramDiscrete
-
- counts - Variable in class etomica.data.histogram.HistogramNotSoSimple
-
- counts - Variable in class etomica.data.histogram.HistogramSimple
-
- counts - Variable in class etomica.metastable.MeterDensityDistribution
-
- coupledMove - Variable in class etomica.models.hexane.TestHexane
-
- coupledMove - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- coupledMove - Variable in class etomica.models.hexane.TestSetToUHexane
-
- covalent - Static variable in class org.jmol.script.Token
-
- covalentMars - Static variable in class org.jmol.util.Elements
-
Default table of covalent Radii
stored as a short mar ...
- COVARIANCE - Static variable in class etomica.data.AccumulatorAverageCovariance
-
- covariance - Variable in class etomica.data.AccumulatorAverageCovariance
-
- covSum - Variable in class etomica.data.AccumulatorAverageCovariance
-
- cp - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
-
- cPairID - Variable in class etomica.virial.BoxCluster
-
- cPairID - Variable in class etomica.virial.ClusterChainHS
-
- cPairID - Variable in class etomica.virial.ClusterChainSoft
-
- cPairID - Variable in class etomica.virial.ClusterCoupledFlipped
-
- cPairID - Variable in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- cPairID - Variable in class etomica.virial.ClusterCoupledFlippedPartial
-
- cPairID - Variable in class etomica.virial.ClusterSinglyConnected
-
- cPairID - Variable in class etomica.virial.ClusterSum
-
- cPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- cPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- cPairID - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- cPairID - Variable in class etomica.virial.ClusterWheatleyHS
-
- cPairID - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- cPairID - Variable in class etomica.virial.ClusterWheatleySoft
-
- cPairID - Variable in class etomica.virial.ClusterWheatleySoftBD
-
- cPairID - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- cPairID - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- cPairSet - Variable in class etomica.virial.BoxCluster
-
- cPairSetTmp - Variable in class etomica.virial.BoxCluster
-
- cPairTrialSet - Variable in class etomica.virial.BoxCluster
-
- crank - Variable in class etomica.models.hexane.TestHexane
-
- crank - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- create - Static variable in class org.jmol.script.Token
-
- createAndShowGUI() - Method in class etomica.units.gui.UnitGraphics
-
- createArrayOfArrayList(int) - Static method in class org.jmol.util.ArrayUtil
-
Helper method for creating a List<T>[]without warnings.
- createArrayOfHashtable(int) - Static method in class org.jmol.util.ArrayUtil
-
Helper method for creating a Map<K, V>[] without warnings.
- createBitmap(String) - Static method in class etomica.graph.model.BitmapFactory
-
- createBitmap(byte[]) - Static method in class etomica.graph.model.BitmapFactory
-
- createBitmap(byte, boolean) - Static method in class etomica.graph.model.BitmapFactory
-
- createCoefficient() - Static method in class etomica.graph.model.GraphFactory
-
- createDataStream(ConstructionParams, String) - Method in class etomica.server.resources.data.DataStreamResource
-
- createDecimalSliderStandardLabels(double) - Method in class etomica.graphics.DecimalSlider
-
- createDisplayBoxPaintAction(Box) - Method in class etomica.graphics.SimulationGraphic
-
- createEdge(byte) - Static method in class etomica.graph.model.GraphFactory
-
- createEdge(byte, char) - Static method in class etomica.graph.model.impl.EdgeImpl
-
- createEdges() - Method in class etomica.graph.model.impl.GraphImpl
-
- createEllipsoidShades() - Static method in class org.jmol.util.Shader
-
- createFieldNode(byte, char) - Static method in class etomica.graph.model.impl.NodeImpl
-
- createFont3D(int, int, float, float, ApiPlatform, Object) - Static method in class org.jmol.util.JmolFont
-
- createGeodesic(int) - Static method in class org.jmol.util.Geodesic
-
- createGraph(byte, Bitmap) - Static method in class etomica.graph.model.GraphFactory
-
- createGraph(byte, byte, Bitmap) - Static method in class etomica.graph.model.GraphFactory
-
- createGraph(byte) - Static method in class etomica.graph.model.GraphFactory
-
- createGraph(Node[]) - Static method in class etomica.graph.model.GraphFactory
-
- createHistograms(DataFork, Dimension, IRandom, IntegratorEventManager, boolean) - Method in class etomica.modules.statistics.StatisticsMCGraphic
-
- createImage(Object) - Method in interface org.jmol.api.ApiPlatform
-
can be ignored (return null) if platform cannot save images
- createImage(Object) - Method in class org.jmol.awt.Platform
-
could be byte[] (from ZIP file) or String (local file name) or URL
- createImageIcon(String) - Static method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- createImageIcon(String) - Static method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- createInnerIterator() - Method in class etomica.graph.iterators.CartesianIterator
-
- createInnerIterator() - Method in class etomica.graph.iterators.PartitionedIterator
-
- createInnerPermutator() - Method in class etomica.graph.iterators.CartesianPermutator
-
- createInstance(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
-
Creates an instance of the implementing class based on the given parameters.
- createInstance(int) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- createInstance(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong
-
- createInstance(int) - Method in class etomica.graph.model.impl.BitmapOfLong
-
- createInstance(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- createInstance(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- createInstance(ConstructionParams, SimulationModel) - Static method in class etomica.server.core.construction.Construction
-
- createIntegrators() - Method in class etomica.kmc.IntegratorKMC
-
- createIntegrators() - Method in class etomica.kmc.IntegratorKMCCluster
-
- createNode(byte) - Static method in class etomica.graph.model.GraphFactory
-
- createNode(byte, boolean) - Static method in class etomica.graph.model.GraphFactory
-
- createNode(byte, char, char) - Static method in class etomica.graph.model.GraphFactory
-
- createNode(byte, char, char) - Static method in class etomica.graph.model.impl.NodeImpl
-
- createOffScreen(int, int) - Method in class etomica.graphics.DisplayCanvas
-
- createOuterIterator() - Method in class etomica.graph.iterators.CartesianIterator
-
- createOuterIterator() - Method in class etomica.graph.iterators.IsomorphismPrefilteredPartitionedIterator
-
- createOuterIterator() - Method in class etomica.graph.iterators.PartitionedIterator
-
- createOuterPermutator() - Method in class etomica.graph.iterators.CartesianPermutator
-
- createOutputDir(File) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Creates directories for output files if needed.
- createReverseEdge(byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- createReverseEdges() - Method in interface etomica.graph.model.Graph
-
- createReverseEdges() - Method in class etomica.graph.model.impl.GraphImpl
-
- createRootNode(byte, char) - Static method in class etomica.graph.model.impl.NodeImpl
-
- createSimulation(SimulationConstructor) - Method in class etomica.server.resources.SimulationResource
-
- createSpecies() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- createSpecies() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- createSpecies() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- createSpecies() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- createSpecies() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- createSpeciesFactory() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- createSpeciesFactory() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- createStatPanel(DataFork, Dimension, AccumulatorFactory, boolean) - Method in class etomica.modules.statistics.StatisticsMCGraphic
-
- createThreads() - Method in class etomica.threads.AtomDecompositionMD
-
- createView(String, Set<Graph>) - Static method in class etomica.graph.viewer.ClusterViewer
-
- crep - Variable in class etomica.potential.P2HydrogenHinde
-
- crep - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- CRINGS - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- CRINGS - Static variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- CRINGS - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- criterion - Variable in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
-
- criterion - Variable in class etomica.modules.render.RenderMD
-
- criterion - Variable in class etomica.potential.PotentialGroup
-
- criterion3 - Variable in class etomica.modules.sam.Sam
-
- CriterionAdapter - Class in etomica.nbr
-
Wraps another criterion while adding additional criteria to the acceptance
decision.
- CriterionAdapter(NeighborCriterion) - Constructor for class etomica.nbr.CriterionAdapter
-
Constructs criterion that wraps the given criterion.
- CriterionAdapterMolecular - Class in etomica.nbr.molecule
-
Wraps another criterion while adding additional criteria to the acceptance
decision.
- CriterionAdapterMolecular(NeighborCriterionMolecular) - Constructor for class etomica.nbr.molecule.CriterionAdapterMolecular
-
Constructs criterion that wraps the given criterion.
- CriterionAll - Class in etomica.nbr
-
Specifies that all atoms pairs are to be considered neighbors.
- CriterionAll() - Constructor for class etomica.nbr.CriterionAll
-
- CriterionAllMolecular - Class in etomica.nbr.molecule
-
Specifies that all atoms pairs are to be considered neighbors.
- CriterionAllMolecular() - Constructor for class etomica.nbr.molecule.CriterionAllMolecular
-
- CriterionBondedSimple - Class in etomica.nbr
-
- CriterionBondedSimple(NeighborCriterion) - Constructor for class etomica.nbr.CriterionBondedSimple
-
- CriterionCar(ParseObj, Box) - Constructor for class etomica.modules.render.RenderMD.CriterionCar
-
- CriterionInterMolecular - Class in etomica.nbr
-
Pair criterion that judges whether two atoms are or are not in the same
molecule.
- CriterionInterMolecular(NeighborCriterion) - Constructor for class etomica.nbr.CriterionInterMolecular
-
Constructs criterion in default state such that intramolecular pairs are rejected,
and intermolecular pairs are accepted.
- CriterionMolecular - Class in etomica.nbr
-
Pair criterion that judges whether two atoms are or are not in
the same molecule.
- CriterionMolecular(NeighborCriterion) - Constructor for class etomica.nbr.CriterionMolecular
-
Constructs criterion in default state such that intramolecular pairs are rejected,
and intermolecular pairs are accepted.
- CriterionMolecularNonAdjacent - Class in etomica.nbr
-
Pair criterion that judges whether two atoms are or are not in the same
molecule, and whether or not they are separated by a minimum number of bonds.
- CriterionMolecularNonAdjacent(NeighborCriterion) - Constructor for class etomica.nbr.CriterionMolecularNonAdjacent
-
- CriterionNone() - Constructor for class etomica.modules.colloid.ColloidSim.CriterionNone
-
- CriterionNone - Class in etomica.nbr
-
- CriterionNone() - Constructor for class etomica.nbr.CriterionNone
-
- CriterionPositionWall - Class in etomica.nbr
-
Simple neighbor criterion based on distance moved by a leaf atom since
the last update.
- CriterionPositionWall(Simulation) - Constructor for class etomica.nbr.CriterionPositionWall
-
- CriterionPositionWall.DoubleWrapper - Class in etomica.nbr
-
- CriterionSimple - Class in etomica.nbr
-
Simple neighbor criterion based on distance moved by a leaf atom since
the last update.
- CriterionSimple(Simulation, Space, double, double) - Constructor for class etomica.nbr.CriterionSimple
-
- CriterionSimpleMolecular - Class in etomica.nbr.molecule
-
Simple neighbor criterion based on distance between the two molecules
If the molecule moves further than r^2; the update method will kick in
to update the neighborlist.
- CriterionSimpleMolecular(Simulation, Space, double, double) - Constructor for class etomica.nbr.molecule.CriterionSimpleMolecular
-
- CriterionSpecies - Class in etomica.nbr.molecule
-
Filters molecule to match a given species.
- CriterionSpecies(NeighborCriterionMolecular, ISpecies) - Constructor for class etomica.nbr.molecule.CriterionSpecies
-
- CriterionSpeciesPair - Class in etomica.nbr.molecule
-
Filters molecule pairs to match a given pair of Species.
- CriterionSpeciesPair(NeighborCriterionMolecular, ISpecies, ISpecies) - Constructor for class etomica.nbr.molecule.CriterionSpeciesPair
-
- CriterionTether3 - Class in etomica.modules.sam
-
Returns first leaf atom of each polymer molecule and the atom its bonded to.
- CriterionTether3(Simulation, ISpecies, AtomType) - Constructor for class etomica.modules.sam.CriterionTether3
-
- CriterionType - Class in etomica.nbr
-
Filters atoms to match a given AtomType.
- CriterionType(NeighborCriterion, AtomType) - Constructor for class etomica.nbr.CriterionType
-
- CriterionTypePair - Class in etomica.nbr
-
Filters atoms pairs to match a given pair of AtomTypes.
- CriterionTypePair(NeighborCriterion, AtomType, AtomType) - Constructor for class etomica.nbr.CriterionTypePair
-
- CriterionTypesCombination - Class in etomica.nbr
-
Filters AtomSets to match a given set of AtomTypes.
- CriterionTypesCombination(NeighborCriterion, AtomType[]) - Constructor for class etomica.nbr.CriterionTypesCombination
-
- CriterionTypesMulti - Class in etomica.nbr
-
Filters AtomSets to match a given set of AtomTypes.
- CriterionTypesMulti(NeighborCriterion, AtomType[]) - Constructor for class etomica.nbr.CriterionTypesMulti
-
- criterionWallMonomer - Variable in class etomica.modules.colloid.ColloidSim
-
- criticalRho_LJ - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- criticalRho_SF6 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- criticalT_LJ - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- criticalT_SF6 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- cross - Static variable in class org.jmol.script.Token
-
- cross(Vector3f, Vector3f) - Method in class org.jmol.util.Vector3f
-
Sets this vector to be the vector cross product of vectors v1 and v2.
- crossPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- crossVector - Variable in class etomica.virial.MCMoveClusterMoleculeLayerMove
-
- crystal - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- CrystalViewer - Class in etomica.modules.crystalviewer
-
- CrystalViewer() - Constructor for class etomica.modules.crystalviewer.CrystalViewer
-
- CrystalViewer.Applet - Class in etomica.modules.crystalviewer
-
- cs - Variable in class etomica.dimer.P1LepsHarmonic
-
- csp - Static variable in class etomica.potential.P2HydrogenPatkowski
-
- csp - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- cspIso - Static variable in class etomica.potential.P2HydrogenPatkowskiIso
-
- cten - Variable in class etomica.potential.P2HydrogenHinde
-
- cten - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- cType - Variable in class etomica.AlkaneEH.SpeciesMethane
-
- cType - Variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- cType - Variable in class etomica.models.rowley.SpeciesEthanol
-
- cType - Variable in class etomica.models.water.SpeciesWater4PCOM
-
- cType - Variable in class etomica.paracetamol.SpeciesParacetamol
-
- cType - Variable in class etomica.virial.SpeciesAnthracene3site464
-
- cType - Variable in class etomica.virial.SpeciesAnthracene3site545
-
- cType - Variable in class etomica.virial.SpeciesMethane
-
- cType - Variable in class etomica.virial.SpeciesPh3site464
-
- cType - Variable in class etomica.virial.SpeciesPh3site545
-
- cType - Variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- cType - Variable in class etomica.virial.SpeciesTraPPECO2
-
- cType - Variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- cType - Variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- cu - Variable in class etomica.dimer.EnergyMap
-
- cu - Variable in class etomica.meam.MEAM_MC
-
- cu - Variable in class etomica.meam.MEAMMd3D
-
- Cu - Static variable in class etomica.meam.ParameterSetMEAM
-
- cu - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- Cu3Sn - Static variable in class etomica.meam.ParameterSetMEAM
-
- cuAdatom - Variable in class etomica.dimer.EnergyMap
-
- cuB - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- Cube - Class in etomica.math.geometry
-
A geometric cube.
- Cube(Space) - Constructor for class etomica.math.geometry.Cube
-
Constructs a cube of unit size.
- Cube(Space, double) - Constructor for class etomica.math.geometry.Cube
-
Constructs a cube with edge length having the given value.
- cubeRoot(double) - Static method in class etomica.space3d.Vector3D
-
- cubeVertexOffsets - Static variable in class org.jmol.util.BoxInfo
-
- cubeVertexOffsets - Static variable in class org.jmol.util.TriangleData
-
- CubicCentimeter - Class in etomica.units
-
The cubic centimeter unit of volume, cm^3.
- CubicLattice - Interface in etomica.lattice
-
Lattice or crystal with cubic symmetry, such that its spatial size can be
characterized by a single value, the lattice constant.
- CubicMeter - Class in etomica.units
-
The cubic meter unit of volume, m^3.
- Cuboid - Class in etomica.math.geometry
-
A polyhedron composed of three pairs of rectangular faces placed opposite
each other and joined at right angles, also known as a
rectangular parallelepiped.
- Cuboid(Space) - Constructor for class etomica.math.geometry.Cuboid
-
Constructs a cuboid with equal faces of unit size (a cube).
- Cuboid(Space, double, double, double) - Constructor for class etomica.math.geometry.Cuboid
-
Constructs a cuboid with edges of lengths having the given values.
- cuFix - Variable in class etomica.dimer.EnergyMap
-
- cuFixedB - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- cumint - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- cumint(double) - Method in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- cumint - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- cumint(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- cumint - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- cumint(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- cumint - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- cumint(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- Current - Class in etomica.units.dimensions
-
The dimension for electrical current.
- current() - Method in class etomica.units.systems.CGS
-
- current() - Method in class etomica.units.systems.LJ
-
- current() - Method in class etomica.units.systems.MKS
-
- current() - Method in class etomica.units.systems.UnitSystem
-
- current() - Method in class etomica.units.systems.UnitSystem.Sim
-
- currentAction - Variable in class etomica.action.activity.ActivityGroupSeries
-
- currentBlockSum - Variable in class etomica.data.AccumulatorAverageCollapsing
-
- currentBlockSum - Variable in class etomica.data.AccumulatorAverageFixed
-
- currentBlockSum - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- currentBox - Variable in class etomica.graphics.DisplayTextBoxesCAE
-
- currentCores - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- currentKineticEnergy - Variable in class etomica.integrator.IntegratorMD
-
- currentLattice - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- currentlocalpath - Static variable in class org.jmol.script.Token
-
- currentlyRendering() - Method in class org.jmol.g3d.Graphics3D
-
- currentPotentialEnergy - Variable in class etomica.integrator.IntegratorBox
-
- currentTime - Variable in class etomica.integrator.IntegratorMD
-
- currentWells - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- cursor - Variable in class etomica.atom.iterator.ApiIndexList
-
- cursor - Variable in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Index of element to be returned by subsequent call to next.
- cursor - Variable in class etomica.atom.iterator.TripletInnerSequential
-
- cursor - Variable in class etomica.data.history.HistoryCollapsing
-
- cursor - Variable in class etomica.data.history.HistoryScrolling
-
- cursor - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- cursor - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- cursor - Variable in class etomica.lattice.RectangularLatticeNbrIterator
-
- cursor - Variable in class etomica.modules.sam.CriterionTether3
-
- cursor - Variable in class etomica.molecule.iterator.MoleculeIteratorArrayListSimple
-
Index of element to be returned by subsequent call to next.
- CURSOR_CROSSHAIR - Static variable in class org.jmol.viewer.JmolConstants
-
- CURSOR_DEFAULT - Static variable in class org.jmol.viewer.JmolConstants
-
- CURSOR_HAND - Static variable in class org.jmol.viewer.JmolConstants
-
- CURSOR_MOVE - Static variable in class org.jmol.viewer.JmolConstants
-
- CURSOR_WAIT - Static variable in class org.jmol.viewer.JmolConstants
-
- CURSOR_ZOOM - Static variable in class org.jmol.viewer.JmolConstants
-
- curvature - Variable in class etomica.dimer.IntegratorDimerRT
-
- customVF - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- cutoff - Variable in class etomica.modules.dcvgcmd.P1WCAWall
-
- cutoff - Variable in class etomica.modules.droplet.AtomFilterLiquid
-
- cutoff - Variable in class etomica.modules.sam.P1WCAWall
-
- cutoff - Variable in class etomica.potential.P2ReactionFieldDipole
-
- cutoff - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- cutoff2 - Variable in class etomica.modules.sam.P1WCAWall
-
- cutoff2 - Variable in class etomica.potential.P2ReactionFieldDipole
-
- cutoff2 - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- cutoff2 - Variable in class etomica.rotation.P2LJDipole
-
- cutoffRatio - Variable in class etomica.potential.P2MoleculeTruncated
-
- cutoffRatio - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- cutoffSq - Variable in class etomica.modules.droplet.AtomFilterLiquid
-
- cutS - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam
-
- cVec - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- cVector - Variable in class etomica.action.BoxInflateAnisotropic
-
- cVectorOld - Variable in class etomica.action.BoxInflateAnisotropic
-
- CVisitor - Class in etomica.graph.traversal
-
This TraversalVisitor visits nodes and keeps track of biconnected
components.
- CVisitor(List<List<Byte>>) - Constructor for class etomica.graph.traversal.CVisitor
-
- CYAN - Static variable in class org.jmol.util.Colix
-
- cycleDrawBoundaryType() - Method in class g3dsys.images.ImageShell
-
Cycles to the next boundary drawing style
- cycles - Variable in class etomica.modules.osmosis.Osmosis
-
- CYLINDER - Static variable in class g3dsys.control.G3DSys
-
- CYLINDER - Static variable in class g3dsys.images.Bond
-
- D() - Method in class etomica.config.ConfigurationLattice.MyLattice
-
- D - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- d - Variable in class etomica.dimer.SimDimerLJadatom
-
- d - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- d - Variable in class etomica.dimer.SimDimerMEAMGB
-
- D - Variable in class etomica.integrator.IntegratorGear4NPH
-
- D - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- d - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- D() - Method in interface etomica.lattice.AbstractLattice
-
Dimension of the lattice.
- D() - Method in class etomica.lattice.BravaisLattice
-
- D() - Method in class etomica.lattice.BravaisLatticeCrystal
-
Returns the spatial dimension + 1.
- D - Variable in class etomica.lattice.crystal.Primitive
-
- D - Variable in class etomica.lattice.RectangularLattice
-
- D() - Method in class etomica.lattice.RectangularLattice
-
- D - Variable in class etomica.lattice.RectangularLatticeNbrIterator
-
- D() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
- D() - Method in class etomica.math.geometry.Hypersphere
-
- D - Variable in class etomica.math.geometry.Polytope
-
- D() - Method in class etomica.math.geometry.Polytope
-
The dimension of this polytope, which is not necessarily the dimension
of the space it is embedded in.
- D() - Method in interface etomica.math.geometry.Shape
-
Returns the spatial dimension of the shape.
- d - Variable in class etomica.math.numerical.PadeApproximation.VirialParam
-
- D - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
-
- D - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
-
- D - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- D - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- D - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
-
- D - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- D - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
-
- d - Variable in class etomica.modules.rheology.MeterNormalStress
-
- D - Variable in class etomica.modules.statistics.StatisticsMCGraphic.StatsParams
-
- D - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- D - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- D - Variable in class etomica.normalmode.SimBennet.SimBennetParam
-
- D - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
-
- D - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
-
- D - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
-
- D - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
-
- D - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
-
- D - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
-
- D - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
-
- D - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
-
- D - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
-
- D - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
-
- D - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
-
- D - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
-
- D - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
-
- D() - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
-
- D() - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
-
- d(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
-
- d(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- d(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
-
- d(int, double, double) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- D - Static variable in class etomica.potential.P3HydrogenManzhos
-
- d - Static variable in class etomica.potential.P3HydrogenManzhos
-
- D() - Method in class etomica.space.Space
-
- D() - Method in interface etomica.space.Tensor
-
- d(int) - Static method in interface etomica.space.Vector
-
Creates a Vector of the given dimension.
- D() - Method in class etomica.space1d.Space1D
-
- D() - Method in class etomica.space1d.Tensor1D
-
- D() - Method in class etomica.space2d.Space2D
-
- D() - Method in class etomica.space2d.Tensor2D
-
- D() - Method in class etomica.space3d.Space3D
-
- D() - Method in class etomica.space3d.Tensor3D
-
- D() - Method in class etomica.spaceNd.TensorND
-
- D - Variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- d0 - Variable in class etomica.potential.P3HydrogenManzhos
-
- d2 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- d2dfac - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- d2f(int[], double[]) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- d2fac - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- d2phi_du2(int[]) - Method in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- d2phi_du2(int[], int[]) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- d2phi_du2(int[], double[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- d2phi_du2(int[], int[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- d2r - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- d2sum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- d2tot - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- d2tot - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- d2tot - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- d2tot - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- d2u(double) - Method in class etomica.models.rowley.P2RepRowley
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.modules.droplet.P2Cohesion
-
- d2u(double) - Method in class etomica.potential.P1HydrogenMielke
-
- d2u(double) - Method in interface etomica.potential.P1IntraMolecular
-
- d2u(double) - Method in class etomica.potential.P2Anharmonic
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2ArgonAziz1993
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2ArgonSlavicekEtAl2003
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2ArgonTangAndToennies2003
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
-
- d2u(double) - Method in class etomica.potential.P2Dreiding
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2Electrostatic
-
- d2u(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
- d2u(double) - Method in class etomica.potential.P2Exp6
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2Exp6Buckingham
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2Fene
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2Harmonic
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2HePCKLJS
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2HeSimplified
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
-
- d2u(double) - Method in class etomica.potential.P2LennardJones
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2LennardJonesDreiding
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2LJQQ
-
- d2u(double) - Method in class etomica.potential.P2ModifiedMorse
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2Morse
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2QChemInterpolated
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2SoftSphere
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.P2SoftSphericalTruncated
-
Returns the 2nd derivative (r^2 d^2u/dr^2) of the wrapped potential if the separation
is less than the cutoff value
- d2u(double) - Method in class etomica.potential.P2WCA
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.potential.Potential2SoftSpherical
-
The second derivative of the pair energy, times the square of the
separation: r^2 d^2u/dr^2.
- d2u(double) - Method in class etomica.virial.P1IntraLambda
-
- d2u(double) - Method in class etomica.yukawa.P2HC2Yukawa
-
- d2u(double) - Method in class etomica.yukawa.P2Yukawa
-
r^2 * d^2u/dr^2 method.
- d2uCorrection(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
-
Uses result from integration-by-parts to evaluate integral of
r2 d2u/dr2 using integral of u.
- d3dfac - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- d3fac - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- D4 - Static variable in class etomica.virial.cluster.Standard
-
- D5 - Static variable in class etomica.virial.cluster.Standard
-
- D6 - Static variable in class etomica.virial.cluster.Standard
-
- dab - Variable in class etomica.dimer.P1LepsHarmonic
-
- dac - Variable in class etomica.dimer.P1LepsHarmonic
-
- dAcc - Variable in class etomica.spin.Heisenberg
-
- dadbSum - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
-
- dadbSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- dadbSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- daDef - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- daDef - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
-
- daDef - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- Dalton - Class in etomica.units
-
- damp(int, double, double) - Method in class etomica.models.water.P2WaterSzalewicz
-
- DampingParams() - Constructor for class etomica.potential.P2QChemInterpolated.DampingParams
-
- DampingParams() - Constructor for class etomica.potential.P3AdditiveQChem.DampingParams
-
- DampingParams() - Constructor for class etomica.potential.P3QChem.DampingParams
-
- DampingParams() - Constructor for class etomica.virial.B3ForSphericallySymmetricU.DampingParams
-
- DASH_MAP - Static variable in interface etomica.graph.model.Metadata
-
- daSpan - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- data - Variable in class etomica.data.AccumulatorCounter
-
- data - Variable in class etomica.data.DataDump
-
- data - Variable in class etomica.data.DataProcessorChemicalPotential
-
- data - Variable in class etomica.data.DataProcessorFunction
-
- data - Variable in class etomica.data.DataProcessorInterfacialTension
-
- data - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
-
- data - Variable in class etomica.data.DataSourceScalar
-
- data - Variable in class etomica.data.DataSourceTensorVirialHard
-
- data - Variable in class etomica.data.meter.MeterDihedralAngle
-
- data - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- data - Variable in class etomica.data.meter.MeterHyperVirial
-
- data - Variable in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
-
- data - Variable in class etomica.data.meter.MeterPressureTensor
-
- data - Variable in class etomica.data.meter.MeterPressureTensorFromIntegrator
-
- data - Variable in class etomica.data.meter.MeterProfileByAtoms
-
- data - Variable in class etomica.data.meter.MeterProfileByVolume
-
- data - Variable in class etomica.data.meter.MeterRDF
-
- data - Variable in class etomica.data.meter.MeterRDFPC
-
- data - Variable in class etomica.data.meter.MeterStructureFactor
-
- data - Variable in class etomica.data.types.DataGroup
-
- data - Variable in class etomica.freeenergy.npath.DataSourceEnergies
-
- data - Variable in class etomica.gaussianwork.MeterBoltzmannA
-
- data - Variable in class etomica.gaussianwork.MeterBoltzmannB
-
- data - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- data - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- data - Variable in class etomica.liquidLJ.DataProcessorReweight
-
- data - Variable in class etomica.liquidLJ.DataProcessorReweightRatio
-
- data - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
-
- data - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- data - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- data - Variable in class etomica.liquidLJ.MeterPU
-
- data - Variable in class etomica.liquidLJ.MeterPUCut
-
- data - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- data - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- data - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- data - Variable in class etomica.mappedvirial.MeterMeanForce
-
- data - Variable in class etomica.metastable.DataProcessorXY
-
- data - Variable in class etomica.models.nitrogen.MeterBoltzmann
-
- data - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- data - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- data - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- data - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
-
- data - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- data - Variable in class etomica.modules.chainequilibrium.MeterChainLength
-
- data - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg
-
- data - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg2
-
- data - Variable in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
-
- data - Variable in class etomica.modules.droplet.MeterDeformation
-
- data - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- data - Variable in class etomica.modules.entropylottery.EntropyProcessor
-
- data - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- data - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
-
- data - Variable in class etomica.modules.interfacial.MeterOrientation
-
- data - Variable in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
-
- data - Variable in class etomica.modules.mu.DataSourceWallPressureMu
-
- data - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
-
- data - Variable in class etomica.modules.multiharmonic.DataProcessorBias
-
- data - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
-
- data - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- data - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- data - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
-
- data - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- data - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- data - Variable in class etomica.modules.rosmosis.MeterFlux
-
- data - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
-
- data - Variable in class etomica.modules.sam.MeterTilt
-
- data - Variable in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
-
- data - Variable in class etomica.modules.statistics.DataCollector
-
- data - Variable in class etomica.modules.statistics.DataProcessorMu
-
- data - Variable in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- data - Variable in class etomica.normalmode.DataProcessorBoltzmannFactor
-
- data - Variable in class etomica.normalmode.DataSourceFE
-
- data - Variable in class etomica.normalmode.DataSourceFEHistogram
-
- data - Variable in class etomica.normalmode.DataSourceImposedFEFit
-
- data - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
-
- data - Variable in class etomica.normalmode.DataSourcePMu
-
- data - Variable in class etomica.normalmode.DataSourcePN
-
- data - Variable in class etomica.normalmode.MeterBoltzmann
-
- data - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
-
- data - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- data - Variable in class etomica.normalmode.MeterBoltzmannTarget
-
- data - Variable in class etomica.normalmode.MeterDADB
-
- data - Variable in class etomica.normalmode.MeterDDP
-
- data - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- data - Variable in class etomica.normalmode.MeterDirectSamplingTarget
-
- data - Variable in class etomica.normalmode.MeterDP
-
- data - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- data - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- data - Variable in class etomica.normalmode.MeterPlaneSlip
-
- data - Variable in class etomica.normalmode.MeterSamplingHarmonic
-
- data - Variable in class etomica.normalmode.MeterSamplingTarget
-
- data - Variable in class etomica.normalmode.MeterSolidDA
-
- data - Variable in class etomica.normalmode.MeterSolidDACut
-
- data - Variable in class etomica.normalmode.MeterSolidMirror
-
- data - Variable in class etomica.normalmode.MeterSolidProps
-
- data - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- data - Variable in class etomica.normalmode.MeterTargetTP
-
- data - Variable in class etomica.normalmode.MeterTilt
-
- data - Variable in class etomica.normalmode.MeterTiltHistogram
-
- data - Variable in class etomica.normalmode.MeterTiltRotation
-
- data - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- data - Variable in class etomica.normalmode.MeterTiltRotationStdev
-
- data - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
-
- data - Variable in class etomica.normalmode.MeterWorkBennetTarget
-
- data - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
-
- data - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- data - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- data - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- data - Variable in class etomica.normalmode.MeterWorkTargetBennet
-
- data - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- data - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- data - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
-
- data - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- data - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- data - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- data - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- data - Variable in class etomica.overlap.MeterOverlap
-
- data - Variable in class etomica.surfacetension.DataProcessorSurfaceTension
-
- data - Variable in class etomica.surfacetension.SurfaceTensionMapped
-
- data - Variable in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- data - Variable in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- data - Static variable in class org.jmol.script.Token
-
- DataAccCorrectedPusher - Class in etomica.modules.statistics
-
- DataAccCorrectedPusher(int, DataCollector) - Constructor for class etomica.modules.statistics.DataAccCorrectedPusher
-
- DataAccDiffCorrectedPusher - Class in etomica.modules.statistics
-
- DataAccDiffCorrectedPusher(int, DataCollector, AccumulatorAverage) - Constructor for class etomica.modules.statistics.DataAccDiffCorrectedPusher
-
- DataAccDifficultyPusher - Class in etomica.modules.statistics
-
- DataAccDifficultyPusher(int, DataCollector, AccumulatorAverage) - Constructor for class etomica.modules.statistics.DataAccDifficultyPusher
-
- DataAccPusher - Class in etomica.modules.statistics
-
- DataAccPusher(int, DataCollector) - Constructor for class etomica.modules.statistics.DataAccPusher
-
- DataAccSamplesPusher - Class in etomica.modules.statistics
-
- DataAccSamplesPusher(int, DataCollector, AccumulatorAverage) - Constructor for class etomica.modules.statistics.DataAccSamplesPusher
-
- DataAccumulator - Class in etomica.data
-
DataProcessor that accumulates and transforms given data and intermittently transmits
processed data to other DataSink(s).
- DataAccumulator() - Constructor for class etomica.data.DataAccumulator
-
Constructs accumulator with no initial DataSink.
- DataAndInfo - Class in etomica.server.representations
-
- DataAndInfo() - Constructor for class etomica.server.representations.DataAndInfo
-
- DataAndInfoEncoder() - Constructor for class etomica.server.resources.data.DataStreamWebsocket.DataAndInfoEncoder
-
- DataArrayWriter - Class in etomica.data
-
A DataWriter that writes out data as a table with optional column headings
- DataArrayWriter() - Constructor for class etomica.data.DataArrayWriter
-
- databases - Static variable in class org.jmol.viewer.JmolConstants
-
- dataChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSet
-
Notifies the DataSet that new Data has arrived for the given psuedo
DataSink.
- dataChanged(DataSet) - Method in interface etomica.data.DataSetListener
-
Method called when one or more pieces of data have changed.
- dataChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSinkTable
-
- dataChanged(DataSet) - Method in class etomica.graphics.DisplayPlot
-
Causes the display of the plot to be updated.
- dataChanged(DataSet) - Method in class etomica.graphics.DisplayTable
-
Causes the display of the plot to be updated.
- DataCollector - Class in etomica.modules.statistics
-
- DataCollector() - Constructor for class etomica.modules.statistics.DataCollector
-
- dataCountChanged(DataSet) - Method in interface etomica.data.DataSetListener
-
Method called when a Data object is added.
- dataCountChanged(DataSet) - Method in class etomica.graphics.DisplayPlot
-
Updates the units array for the new column, using the default units.
- dataCountChanged(DataSet) - Method in class etomica.graphics.DisplayTable
-
Updates the units array for any new or deleted columns,
using the default units for new columns.
- DataCutter - Class in etomica.zeolite
-
- DataCutter(String, int) - Constructor for class etomica.zeolite.DataCutter
-
- dataDistance - Variable in class etomica.virial.MeterSamplingWeight
-
- DataDistributer - Class in etomica.data
-
DataSink that takes a Data object and pushes it to a dataSink chosen
by an indexer.
- DataDistributer(DataDistributer.Indexer, DataSplitter.IDataSinkFactory) - Constructor for class etomica.data.DataDistributer
-
- DataDistributer.Indexer - Interface in etomica.data
-
- DataDouble - Class in etomica.data.types
-
Data object wrapping a single mutable value of type double.
- DataDouble() - Constructor for class etomica.data.types.DataDouble
-
Constructs a new instance with given descriptors.
- DataDouble.DataInfoDouble - Class in etomica.data.types
-
- DataDouble.DataInfoDoubleFactory - Class in etomica.data.types
-
- DataDoubleArray - Class in etomica.data.types
-
Data object that wraps a mutable array of doubles.
- DataDoubleArray(int) - Constructor for class etomica.data.types.DataDoubleArray
-
Constructs a new one-dimensional array of the given length.
- DataDoubleArray(int[]) - Constructor for class etomica.data.types.DataDoubleArray
-
Constructs a new multidimensional array of the given shape.
- DataDoubleArray(int[], double[]) - Constructor for class etomica.data.types.DataDoubleArray
-
Wraps the given array, xData in a DataDoubleArray of the given shape.
- DataDoubleArray.DataInfoDoubleArray - Class in etomica.data.types
-
- DataDoubleArray.DataInfoDoubleArrayFactory - Class in etomica.data.types
-
- DataDoubleBDArray - Class in etomica.data.types
-
Data object that wraps a array of BigDecimals.
- DataDoubleBDArray(int, int) - Constructor for class etomica.data.types.DataDoubleBDArray
-
Constructs a new one-dimensional array of the given length.
- DataDoubleBDArray(int[], int) - Constructor for class etomica.data.types.DataDoubleBDArray
-
Constructs a new multidimensional array of the given shape.
- DataDoubleBDArray.DataInfoDoubleBDArray - Class in etomica.data.types
-
- DataDoubleBDArray.DataInfoDoubleBDArrayFactory - Class in etomica.data.types
-
- DataDump - Class in etomica.data
-
DataDump acts both as a DataSink and a DataSource.
- DataDump() - Constructor for class etomica.data.DataDump
-
- dataDy - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- dataDy - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- dataDy2 - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- dataDy2 - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- dataDy3 - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- dataEVec - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- dataEy - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- dataEy - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- DataFork - Class in etomica.data
-
DataSink that takes a data stream and forwards it across multiple sinks.
- DataFork() - Constructor for class etomica.data.DataFork
-
Constructs with no initial DataSinks.
- DataFork(IDataSink[]) - Constructor for class etomica.data.DataFork
-
Constructs to forward data to the given sinks.
- DataFunction - Class in etomica.data.types
-
Collects two or more DataDoubleArray instances, and organizes them into
"dependent" and "independent" subgroups.
- DataFunction(int[], double[]) - Constructor for class etomica.data.types.DataFunction
-
Forms a DataFunction using the given independent and dependent data
instances.
- DataFunction(int[]) - Constructor for class etomica.data.types.DataFunction
-
Forms a DataFunction with the given array shape.
- DataFunction.DataInfoFunction - Class in etomica.data.types
-
- DataFunction.DataInfoFunctionFactory - Class in etomica.data.types
-
- dataGroup - Variable in class etomica.data.AccumulatorAverage
-
- dataGroup - Variable in class etomica.data.AccumulatorAverageBlockless
-
- DataGroup - Class in etomica.data.types
-
Gathers one or more Data instances into a single Data object.
- DataGroup(IData[]) - Constructor for class etomica.data.types.DataGroup
-
Forms a data group from the given array of data objects.
- dataGroup - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- DataGroup.DataInfoGroup - Class in etomica.data.types
-
- DataGroup.DataInfoGroupFactory - Class in etomica.data.types
-
- DataGroupFilter - Class in etomica.data
-
Extracts one or more of the Data instances wrapped in a DataGroup.
- DataGroupFilter(int) - Constructor for class etomica.data.DataGroupFilter
-
Creates a filter that will take the DataGroup element indicated
by the index, counting from 0.
- DataGroupFilter(int[]) - Constructor for class etomica.data.DataGroupFilter
-
Creates a filter that will take the set of elements from the DataGroup
corresponding to the given index values (with indexes counting from 0).
- DataGroupSplitter - Class in etomica.data
-
DataSink that takes a DataGroup object and pushes each sub-Data object from
the incoming DataGroup to a different stream.
- DataGroupSplitter() - Constructor for class etomica.data.DataGroupSplitter
-
- dataInfo - Variable in class etomica.data.DataDistributer
-
- dataInfo - Variable in class etomica.data.DataDump
-
- dataInfo - Variable in class etomica.data.DataFork
-
- DataInfo - Class in etomica.data
-
Object associated with a Data instance and which provides descriptive
information about the data encapsulated in it.
- DataInfo(String, Dimension) - Constructor for class etomica.data.DataInfo
-
Constructs new instance with descriptive label and dimension.
- dataInfo - Variable in class etomica.data.DataProcessor
-
- dataInfo - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
-
- dataInfo - Variable in class etomica.data.DataSourceScalar
-
- dataInfo - Variable in class etomica.data.DataSourceTensorVirialHard
-
- dataInfo - Variable in class etomica.data.DataSplitter
-
- dataInfo - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- dataInfo - Variable in class etomica.data.meter.MeterHyperVirial
-
- dataInfo - Variable in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
-
- dataInfo - Variable in class etomica.data.meter.MeterPressureTensor
-
- dataInfo - Variable in class etomica.data.meter.MeterPressureTensorFromIntegrator
-
- dataInfo - Variable in class etomica.data.meter.MeterProfileByAtoms
-
- dataInfo - Variable in class etomica.data.meter.MeterProfileByVolume
-
- dataInfo - Variable in class etomica.data.meter.MeterStructureFactor
-
- dataInfo - Variable in class etomica.freeenergy.npath.DataSourceEnergies
-
- dataInfo - Variable in class etomica.gaussianwork.MeterBoltzmannA
-
- dataInfo - Variable in class etomica.gaussianwork.MeterBoltzmannB
-
- dataInfo - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- dataInfo - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- dataInfo - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- dataInfo - Variable in class etomica.liquidLJ.MeterPU
-
- dataInfo - Variable in class etomica.liquidLJ.MeterPUCut
-
- dataInfo - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- dataInfo - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
Number of insertions attempted in each call to currentValue Default is
100
- dataInfo - Variable in class etomica.mappedvirial.MeterMeanForce
-
- dataInfo - Variable in class etomica.models.nitrogen.MeterBoltzmann
-
- dataInfo - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- dataInfo - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- dataInfo - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- dataInfo - Variable in class etomica.models.oneDHardRods.MeterNMCBaskets
-
- dataInfo - Variable in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
-
- dataInfo - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
-
- dataInfo - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- dataInfo - Variable in class etomica.modules.chainequilibrium.MeterChainLength
-
- dataInfo - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg
-
- dataInfo - Variable in class etomica.modules.chainequilibrium.MolecularWeightAvg2
-
- dataInfo - Variable in class etomica.modules.droplet.MeterDeformation
-
- dataInfo - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- dataInfo - Variable in class etomica.modules.interfacial.MeterOrientation
-
- dataInfo - Variable in class etomica.modules.mu.DataSourceWallPressureMu
-
- dataInfo - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
-
- dataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorBias
-
- dataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
-
- dataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- dataInfo - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- dataInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- dataInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- dataInfo - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- dataInfo - Variable in class etomica.modules.rosmosis.MeterFlux
-
- dataInfo - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
-
- dataInfo - Variable in class etomica.modules.sam.MeterTilt
-
- dataInfo - Variable in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
-
- dataInfo - Variable in class etomica.modules.statistics.DataCollector
-
- dataInfo - Variable in class etomica.normalmode.DataProcessorBoltzmannFactor
-
- dataInfo - Variable in class etomica.normalmode.DataSourceFE
-
- dataInfo - Variable in class etomica.normalmode.DataSourceFEHistogram
-
- dataInfo - Variable in class etomica.normalmode.DataSourceImposedFEFit
-
- dataInfo - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
-
- dataInfo - Variable in class etomica.normalmode.DataSourcePMu
-
- dataInfo - Variable in class etomica.normalmode.DataSourcePN
-
- dataInfo - Variable in class etomica.normalmode.MeterBoltzmann
-
- dataInfo - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
-
- dataInfo - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- dataInfo - Variable in class etomica.normalmode.MeterBoltzmannTarget
-
- dataInfo - Variable in class etomica.normalmode.MeterDADB
-
- dataInfo - Variable in class etomica.normalmode.MeterDDP
-
- dataInfo - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- dataInfo - Variable in class etomica.normalmode.MeterDirectSamplingTarget
-
- dataInfo - Variable in class etomica.normalmode.MeterDP
-
- dataInfo - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- dataInfo - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- dataInfo - Variable in class etomica.normalmode.MeterPlaneSlip
-
- dataInfo - Variable in class etomica.normalmode.MeterSamplingHarmonic
-
- dataInfo - Variable in class etomica.normalmode.MeterSamplingTarget
-
- dataInfo - Variable in class etomica.normalmode.MeterSolidDA
-
- dataInfo - Variable in class etomica.normalmode.MeterSolidDACut
-
- dataInfo - Variable in class etomica.normalmode.MeterSolidMirror
-
- dataInfo - Variable in class etomica.normalmode.MeterSolidProps
-
- dataInfo - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- dataInfo - Variable in class etomica.normalmode.MeterTargetTP
-
- dataInfo - Variable in class etomica.normalmode.MeterTilt
-
- dataInfo - Variable in class etomica.normalmode.MeterTiltHistogram
-
- dataInfo - Variable in class etomica.normalmode.MeterTiltRotation
-
- dataInfo - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- dataInfo - Variable in class etomica.normalmode.MeterTiltRotationStdev
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkBennetTarget
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkTargetBennet
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- dataInfo - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- dataInfo - Variable in class etomica.overlap.MeterOverlap
-
- dataInfo - Variable in class etomica.surfacetension.DataProcessorSurfaceTension
-
- dataInfoA - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- dataInfoA - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- dataInfoA - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- dataInfoChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSet
-
Notifies the DataSet that new DataInfo has arrived for the given
psuedo DataSink.
- dataInfoChanged(DataSet.DataSetSink) - Method in class etomica.data.DataSinkTable
-
- DataInfoDouble(String, Dimension) - Constructor for class etomica.data.types.DataDouble.DataInfoDouble
-
- DataInfoDoubleArray(String, Dimension, int[]) - Constructor for class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
-
- DataInfoDoubleArrayFactory(DataDoubleArray.DataInfoDoubleArray) - Constructor for class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory
-
- DataInfoDoubleBDArray(String, Dimension, int[], int) - Constructor for class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
-
- DataInfoDoubleBDArrayFactory(DataDoubleBDArray.DataInfoDoubleBDArray) - Constructor for class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
-
- DataInfoDoubleFactory(DataDouble.DataInfoDouble) - Constructor for class etomica.data.types.DataDouble.DataInfoDoubleFactory
-
- DataInfoFactory - Class in etomica.data
-
Interface for a mutable DataInfo factory.
- DataInfoFactory(IDataInfo) - Constructor for class etomica.data.DataInfoFactory
-
Creates a new instance using the info held by the template.
- DataInfoFunction(String, Dimension, DataSourceIndependent) - Constructor for class etomica.data.types.DataFunction.DataInfoFunction
-
- DataInfoFunctionFactory(DataFunction.DataInfoFunction) - Constructor for class etomica.data.types.DataFunction.DataInfoFunctionFactory
-
- dataInfoGroup - Variable in class etomica.data.DataGroupSplitter
-
- DataInfoGroup(String, Dimension, IDataInfo[]) - Constructor for class etomica.data.types.DataGroup.DataInfoGroup
-
- dataInfoGroup - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- DataInfoGroupFactory(DataGroup.DataInfoGroup) - Constructor for class etomica.data.types.DataGroup.DataInfoGroupFactory
-
- DataInfoTable(String, IDataInfo[], int, String[]) - Constructor for class etomica.data.types.DataTable.DataInfoTable
-
- DataInfoTableFactory(DataTable.DataInfoTable) - Constructor for class etomica.data.types.DataTable.DataInfoTableFactory
-
- DataInfoTensor(String, Dimension, Space) - Constructor for class etomica.data.types.DataTensor.DataInfoTensor
-
- DataInfoTensorFactory(DataTensor.DataInfoTensor) - Constructor for class etomica.data.types.DataTensor.DataInfoTensorFactory
-
- DataInfoVector(String, Dimension, Space) - Constructor for class etomica.data.types.DataVector.DataInfoVector
-
- DataInfoVectorFactory(DataVector.DataInfoVector) - Constructor for class etomica.data.types.DataVector.DataInfoVectorFactory
-
- dataInterval - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- dataInterval - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- DataLogger - Class in etomica.data
-
DataSink that manages a FileWriter and also listens to non-interval
integrator events and sends appropriate data to a DataWriter.
- DataLogger() - Constructor for class etomica.data.DataLogger
-
- DataLogger.DataWriter - Interface in etomica.data
-
Interface for a DataSink that actually writes data to a file
- dataOverlap - Variable in class etomica.normalmode.SimOverlapModule
-
- DataOverlap - Class in etomica.overlap
-
Utility class for overlap sampling.
- DataOverlap(DataOverlap.DataSourceOverlapAvg, DataOverlap.DataSourceOverlapAvg, AlphaSource) - Constructor for class etomica.overlap.DataOverlap
-
- DataOverlap.DataSourceOverlapAvg - Interface in etomica.overlap
-
Interface for a class capable of return the average and uncertainty for
a particular value of alpha.
- DataOverlap.DataSourceOverlapAvgCollapsing - Class in etomica.overlap
-
Implementation of DataSourceOverlapLogAvg that retrieves data from a
splitter whose data is dumped into different
AccumulatorAverageCollapsingLog instances.
- DataOverlap.DataSourceOverlapAvgCollapsingSplit - Class in etomica.overlap
-
- DataOverlap.DataSourceOverlapAvgSimple - Class in etomica.overlap
-
Implementation of DataSourceOverlapAvg that retrieves data from a single
AccumulatorAverage
- DataOverlap.DataSourceOverlapLogAvg - Interface in etomica.overlap
-
Interface for a class capable of return the average and uncertainty as
well as the log of the average and the uncertainty in the log, for
a particular value of alpha.
- DataOverlapCaching - Class in etomica.modules.multiharmonic.overlap
-
DataOverlap subclass that caches return values.
- DataOverlapCaching(DataOverlap.DataSourceOverlapAvg, DataOverlap.DataSourceOverlapAvg, AlphaSource, IntegratorOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.DataOverlapCaching
-
- DataPipe - Interface in etomica.data
-
Interface for an object through which data can flow.
- DataPipeForked - Interface in etomica.data
-
- DataPipeStressStrain(Sam) - Constructor for class etomica.modules.sam.SamGraphic.DataPipeStressStrain
-
- DataPlumbing(DataPumpListener, DataDump, UUID) - Constructor for class etomica.server.dao.DataStreamStore.DataPlumbing
-
- DataProcessAHT(MultiharmonicGraphicMC.DataSourceUa, HistoryCollapsingDiscard) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
-
- DataProcessor - Class in etomica.data
-
An object that receives Data, processes it, and pushes the result on to a
DataSink.
- DataProcessor() - Constructor for class etomica.data.DataProcessor
-
- DataProcessorBias - Class in etomica.modules.multiharmonic
-
Data Processor which calculates the bias in the incoming data based on the
true value of the free energy calculated from the
- DataProcessorBias(DataSourceScalar) - Constructor for class etomica.modules.multiharmonic.DataProcessorBias
-
- DataProcessorBoltzmannFactor - Class in etomica.normalmode
-
- DataProcessorBoltzmannFactor() - Constructor for class etomica.normalmode.DataProcessorBoltzmannFactor
-
- DataProcessorBounds - Class in etomica.modules.multiharmonic
-
Calculates upper or lower bound of the incoming data based on the standard
deviation obtained from the accumulator.
- DataProcessorBounds() - Constructor for class etomica.modules.multiharmonic.DataProcessorBounds
-
- DataProcessorBounds - Class in etomica.modules.statistics
-
- DataProcessorBounds(IDataSink[]) - Constructor for class etomica.modules.statistics.DataProcessorBounds
-
- DataProcessorChemicalPotential - Class in etomica.data
-
DataProcessor that takes as input the average density and average Boltzmann
factor profiles and calculates the chemical potential profile as the sum of
the ideal gas contribution (kT ln()) and the excess chemical
potential, (-kT ln()).
- DataProcessorChemicalPotential() - Constructor for class etomica.data.DataProcessorChemicalPotential
-
- DataProcessorCorrection(int) - Constructor for class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
-
- DataProcessorCvMD - Class in etomica.meam
-
- DataProcessorCvMD() - Constructor for class etomica.meam.DataProcessorCvMD
-
- DataProcessorDyDLnx - Class in etomica.modules.multiharmonic
-
Calculates dy/dlnx vs.
- DataProcessorDyDLnx() - Constructor for class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- DataProcessorFoo() - Constructor for class etomica.models.hexane.TestHexaneHarmonic.DataProcessorFoo
-
- DataProcessorForked - Class in etomica.data
-
A DataProcessor that can handle multiple sinks, passing the same Data to each.
- DataProcessorForked() - Constructor for class etomica.data.DataProcessorForked
-
- DataProcessorFunction - Class in etomica.data
-
Applies a simple scalar function to all elements of the Data
that passes through.
- DataProcessorFunction(IFunction) - Constructor for class etomica.data.DataProcessorFunction
-
- DataProcessorInterfacialTension - Class in etomica.data
-
Data Processor that takes the virial components as input data and returns
the interfacial tension.
- DataProcessorInterfacialTension(Space) - Constructor for class etomica.data.DataProcessorInterfacialTension
-
- DataProcessorInterfacialTensionProfile - Class in etomica.modules.interfacial
-
- DataProcessorInterfacialTensionProfile(Space) - Constructor for class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- DataProcessorMu(AccumulatorHistory, IntegratorBox) - Constructor for class etomica.modules.mu.MuGraphic.DataProcessorMu
-
- DataProcessorMu - Class in etomica.modules.statistics
-
DataProcessor that takes in and spits out
mu = -T*ln
- DataProcessorMu(IntegratorBox) - Constructor for class etomica.modules.statistics.DataProcessorMu
-
- DataProcessorPhi - Class in etomica.densityofstate
-
- DataProcessorPhi() - Constructor for class etomica.densityofstate.DataProcessorPhi
-
- DataProcessorR2() - Constructor for class etomica.virial.simulations.VirialPolyhedra.DataProcessorR2
-
- DataProcessorR2() - Constructor for class etomica.virial.simulations.VirialPolyhedra2.DataProcessorR2
-
- DataProcessorReweight - Class in etomica.liquidLJ
-
Takes incoming data, computes weight for configuration based on various
cutoffs, multiplies each incoming data by the weight and also adds
weights as extra data.
- DataProcessorReweight(double, ValueCache, double[], Box, int) - Constructor for class etomica.liquidLJ.DataProcessorReweight
-
- DataProcessorReweight(double, LjMd3D.ValueCache, LjMd3D.ValueCache, double, double, double, Box, IFunction) - Constructor for class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- DataProcessorReweightRatio - Class in etomica.liquidLJ
-
Takes incoming data sums including a weight sum for each cutoff,
computes averages as sum/(weight sum)
- DataProcessorReweightRatio(int) - Constructor for class etomica.liquidLJ.DataProcessorReweightRatio
-
- DataProcessorReweightRatio(int, int) - Constructor for class etomica.liquidLJ.DataProcessorReweightRatio
-
- DataProcessorSum - Class in etomica.normalmode
-
DataProcessor that sends on the sum of the incoming data values as a scalar.
- DataProcessorSum() - Constructor for class etomica.normalmode.DataProcessorSum
-
- DataProcessorSurfaceTension - Class in etomica.surfacetension
-
- DataProcessorSurfaceTension() - Constructor for class etomica.surfacetension.DataProcessorSurfaceTension
-
- DataProcessorTensorSplitter() - Constructor for class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
-
- DataProcessorTensorSplitter() - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
-
- DataProcessorTensorTrace() - Constructor for class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
-
- DataProcessorUndo(double) - Constructor for class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- DataProcessorVar - Class in etomica.modules.multiharmonic
-
Data Processor whose sole purpose in life is to discard the incoming data
and push on the standard deviation from the accumulator.
- DataProcessorVar() - Constructor for class etomica.modules.multiharmonic.DataProcessorVar
-
- DataProcessorVirialOverlap - Class in etomica.virial.overlap
-
DataProcessor which takes in values for v/pi and pi2/pi (from MeterVirial)
and calculates the overlap values for various values of alpha.
- DataProcessorVirialOverlap(int, boolean) - Constructor for class etomica.virial.overlap.DataProcessorVirialOverlap
-
- DataProcessorXY - Class in etomica.metastable
-
- DataProcessorXY(DataDump) - Constructor for class etomica.metastable.DataProcessorXY
-
- DataPump - Class in etomica.data
-
A DataProcessor whose action is to actively take Data from a DataSource and send it to
DataSinks.
- DataPump(IDataSource, IDataSink) - Constructor for class etomica.data.DataPump
-
Constructs DataPump with the given DataSource and
DataSink.
- dataPump - Variable in class etomica.graphics.DisplayTimer
-
- dataPumpA - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- DataPumpListener - Class in etomica.data
-
- DataPumpListener(IDataSource, IDataSink) - Constructor for class etomica.data.DataPumpListener
-
- DataPumpListener(IDataSource, IDataSink, int) - Constructor for class etomica.data.DataPumpListener
-
- DataPumpListenerPow - Class in etomica.data
-
DataPump class that takes data at steps 2^i, i=0,1,2,3...
- DataPumpListenerPow(IDataSource, IDataSink) - Constructor for class etomica.data.DataPumpListenerPow
-
- DataPumpListenerPow(IDataSource, IDataSink, long, int, int) - Constructor for class etomica.data.DataPumpListenerPow
-
- DataPumpListenerPowStrict - Class in etomica.data
-
DataPump class that takes data at steps pow^i, i=0,1,2,3...
- DataPumpListenerPowStrict(IDataSource, IDataSink) - Constructor for class etomica.data.DataPumpListenerPowStrict
-
- DataPumpListenerPowStrict(IDataSource, IDataSink, int) - Constructor for class etomica.data.DataPumpListenerPowStrict
-
- DataPumpListenerSmart - Class in etomica.data
-
Works with an instance of HistoryCollapsingDiscard to only retrieve new data
from the datasource when the history will actually use the data.
- DataPumpListenerSmart(IDataSource, IDataSink, HistoryCollapsingDiscard) - Constructor for class etomica.data.DataPumpListenerSmart
-
- DataPumpListenerSmart(IDataSource, IDataSink, int, HistoryCollapsingDiscard) - Constructor for class etomica.data.DataPumpListenerSmart
-
- dataPumps - Variable in class etomica.data.DataTableAverages
-
- dataPumps - Variable in class etomica.thermointegration.IntegratorThermodynamic
-
- dataseparator - Static variable in class org.jmol.script.Token
-
- DataSerializer - Class in etomica.server.serializers
-
- DataSerializer() - Constructor for class etomica.server.serializers.DataSerializer
-
- DataSet - Class in etomica.data
-
Receives and organizes data from multiple streams.
- DataSet() - Constructor for class etomica.data.DataSet
-
- dataSet - Variable in class etomica.graphics.DisplayPlot
-
- DataSet.DataSetSink - Class in etomica.data
-
A special DataSink used by the DataSet to receive Data and DataInfo
from a single stream.
- DataSetListener - Interface in etomica.data
-
Interface for a class that performs some action in response to
a change in a DataSet instance.
- DataSetSink(DataSet) - Constructor for class etomica.data.DataSet.DataSetSink
-
- dataSink - Variable in class etomica.data.DataProcessor
-
- dataSink - Variable in class etomica.virial.simulations.SimulationVirial
-
- DataSinkConsole - Class in etomica.data
-
Writes data to console or another print stream.
- DataSinkConsole() - Constructor for class etomica.data.DataSinkConsole
-
Makes class using System.out as the default output stream.
- DataSinkConsole(PrintStream) - Constructor for class etomica.data.DataSinkConsole
-
Constructor that permits specification of the output printstream.
- DataSinkExcludeOverlap(Box) - Constructor for class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
-
- DataSinkExcludeOverlap(Box) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
-
- DataSinkExcludeOverlap(Box) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
-
- DataSinkExcludeOverlap() - Constructor for class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
-
- dataSinkFactory - Variable in class etomica.data.DataDistributer
-
- dataSinkFactory - Variable in class etomica.data.DataSplitter
-
- dataSinkList - Variable in class etomica.data.DataFork
-
- DataSinkReweightedDeltaU(AlphaSource) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- dataSinks - Variable in class etomica.data.DataDistributer
-
- dataSinks - Variable in class etomica.data.DataGroupSplitter
-
- dataSinks - Variable in class etomica.data.DataSplitter
-
- DataSinkTable - Class in etomica.data
-
Receives data from multiple streams and organizes it in the form of a table,
with each stream of data forming a column of the table.
- DataSinkTable() - Constructor for class etomica.data.DataSinkTable
-
- dataSource - Variable in class etomica.data.DataPump
-
- dataSourceA - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- DataSourceAcceptanceProbability - Class in etomica.data
-
Data source giving the average acceptance probability of MCMove type moves.
- DataSourceAcceptanceProbability() - Constructor for class etomica.data.DataSourceAcceptanceProbability
-
Constructs with no MCMove specified.
- DataSourceAcceptanceProbability(MCMove) - Constructor for class etomica.data.DataSourceAcceptanceProbability
-
- DataSourceAcceptanceRatio - Class in etomica.data
-
Data source giving the acceptance rate of MCMove type moves.
- DataSourceAcceptanceRatio() - Constructor for class etomica.data.DataSourceAcceptanceRatio
-
Constructs with no MCMove specified.
- DataSourceAcceptanceRatio(MCMove) - Constructor for class etomica.data.DataSourceAcceptanceRatio
-
- DataSourceAlphaAlpha(DataOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- DataSourceAlphaAlpha(DataSourceVirialOverlap) - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- DataSourceAlphaChi(MeterMBAR, MeterMBAR, boolean) - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- DataSourceAlphaChi(DataOverlap, double) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- DataSourceAlphaChi(DataSourceVirialOverlap, double) - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- DataSourceAlphaFE(AlphaSource, int) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- DataSourceAtomDistance - Class in etomica.data
-
- DataSourceAtomDistance(Space) - Constructor for class etomica.data.DataSourceAtomDistance
-
- DataSourceAtomic - Interface in etomica.data
-
Interface for a DataSource that can return a value given an arbitrary atom.
- DataSourceAvgPressure - Class in etomica.normalmode
-
Averages the measured pressures for various N.
- DataSourceAvgPressure(DataDistributer, MCMoveOverlapListener, double) - Constructor for class etomica.normalmode.DataSourceAvgPressure
-
- DataSourceAvgPressure2 - Class in etomica.normalmode
-
Computes pressure from the grand canonical route based on measured free
energy differences and simulation parameters.
- DataSourceAvgPressure2(DataDistributer, MCMoveOverlapListener, double, double) - Constructor for class etomica.normalmode.DataSourceAvgPressure2
-
- dataSourceB - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- DataSourceBias(AlphaSource) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- DataSourceChiSlope(DataOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceChiSlope
-
- DataSourceCollisional - Interface in etomica.data.meter
-
Interface for a meter that can return a value based on a hard-potential collision.
- DataSourceCount() - Constructor for class etomica.data.AccumulatorHistory.DataSourceCount
-
- DataSourceCountCollisions - Class in etomica.data
-
This is a data source to count the number of collisions processed by a
hard-potential integrator.
- DataSourceCountCollisions() - Constructor for class etomica.data.DataSourceCountCollisions
-
Sets up data source with no integrator specified.
- DataSourceCountCollisions(IntegratorHard) - Constructor for class etomica.data.DataSourceCountCollisions
-
- DataSourceCountSteps - Class in etomica.data
-
Data source that fronts the Integrator's step count as a piece of Data.
- DataSourceCountSteps() - Constructor for class etomica.data.DataSourceCountSteps
-
Sets up data source to count integrator steps.
- DataSourceCountSteps(Integrator) - Constructor for class etomica.data.DataSourceCountSteps
-
- DataSourceCountTime - Class in etomica.data
-
Data source that keeps track of the elapsed simulation time of an MD
integrator.
- DataSourceCountTime() - Constructor for class etomica.data.DataSourceCountTime
-
Sets up data source with no integrator specified.
- DataSourceCountTime(IntegratorMD) - Constructor for class etomica.data.DataSourceCountTime
-
- DataSourceDensityFunction - Class in etomica.modules.adsorption
-
- DataSourceDensityFunction(EOSSW, double, double) - Constructor for class etomica.modules.adsorption.DataSourceDensityFunction
-
- DataSourceDensityFunction(EOSSW, double, double, boolean) - Constructor for class etomica.modules.adsorption.DataSourceDensityFunction
-
- DataSourceEnergies - Class in etomica.freeenergy.npath
-
Created by andrew on 4/12/17.
- DataSourceEnergies(PotentialMaster) - Constructor for class etomica.freeenergy.npath.DataSourceEnergies
-
- DataSourceEnergies.PotentialCalculationEnergies - Class in etomica.freeenergy.npath
-
- DataSourceEnergies.PotentialCalculationEnergiesEAM - Class in etomica.freeenergy.npath
-
- DataSourceExp(DataSourceUniform) - Constructor for class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
-
- DataSourceFE(String, MeterMBAR, MeterMBAR, int) - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
-
- DataSourceFE - Class in etomica.normalmode
-
Free energy data source that computes free energy differences based on
overlap sampling performed by an MCMoveOverlapListener.
- DataSourceFE(MCMoveOverlapListener) - Constructor for class etomica.normalmode.DataSourceFE
-
- DataSourceFEHistogram - Class in etomica.normalmode
-
Returns a histogram of # of atoms based on free energy results and the given
chemical potential.
- DataSourceFEHistogram(MCMoveOverlapListener, double) - Constructor for class etomica.normalmode.DataSourceFEHistogram
-
- DataSourceFunction - Class in etomica.data
-
Datasource formed as a wrapper around a function.
- DataSourceFunction() - Constructor for class etomica.data.DataSourceFunction
-
- DataSourceFunction(IFunction) - Constructor for class etomica.data.DataSourceFunction
-
- DataSourceFunction(String, Dimension, IFunction, int) - Constructor for class etomica.data.DataSourceFunction
-
- DataSourceFunction(String, Dimension, IFunction, int, String, Dimension) - Constructor for class etomica.data.DataSourceFunction
-
- DataSourceFunctionRaw(double[], double[]) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- DataSourceGroup - Class in etomica.data
-
Collects one or more data sources into a single DataSource.
- DataSourceGroup() - Constructor for class etomica.data.DataSourceGroup
-
Forms a DataSourceGroup that contains no data sources, and which will give
an empty DataGroup for getData.
- DataSourceGroup(IDataSource[]) - Constructor for class etomica.data.DataSourceGroup
-
Forms a DataGroup containing the given data sources.
- DataSourceImposedFEFit - Class in etomica.normalmode
-
Like DataSourceFEHistogram, returns a probability histogram for N based on
free energies.
- DataSourceImposedFEFit(MCMoveOverlapListener, MCMoveInsertDeleteBiased, double) - Constructor for class etomica.normalmode.DataSourceImposedFEFit
-
- DataSourceImposedFEHistogram - Class in etomica.normalmode
-
This is a strange creature...
- DataSourceImposedFEHistogram(MCMoveOverlapListener, MCMoveInsertDeleteBiased, double) - Constructor for class etomica.normalmode.DataSourceImposedFEHistogram
-
- DataSourceIndependent - Interface in etomica.data
-
Interface for an object that can provide X Data objects on request.
- DataSourceIndependentSimple - Class in etomica.data
-
A simple implementation of DataSourceIndependent objects can use if they
cannot act as the DataSourceIndependent themselves (if perhaps they make
multiple DataFunctions)
- DataSourceIndependentSimple(double[], DataDoubleArray.DataInfoDoubleArray) - Constructor for class etomica.data.DataSourceIndependentSimple
-
- DataSourceIndependentSimple(double[][], DataDoubleArray.DataInfoDoubleArray[]) - Constructor for class etomica.data.DataSourceIndependentSimple
-
- DataSourceIndex - Class in etomica.meta
-
- DataSourceIndex(Class<IDataSource>) - Constructor for class etomica.meta.DataSourceIndex
-
- dataSourceInfo - Variable in class etomica.data.DataPump
-
- DataSourceMolecular - Interface in etomica.data
-
Interface for a DataSource that can return a value given an arbitrary atom.
- DataSourceMuRoot - Class in etomica.normalmode
-
Datasource that returns an estimate of mu based on thermodynamic
self-consistency of pressure measurements and defect free energies.
- DataSourceMuRoot(MCMoveOverlapListener, double, DataDistributer, double, double, double) - Constructor for class etomica.normalmode.DataSourceMuRoot
-
- DataSourceMuRoot.DataSourceMuRootDPressure - Class in etomica.normalmode
-
- DataSourceMuRoot.DataSourceMuRootDU - Class in etomica.normalmode
-
- DataSourceMuRoot.DataSourceMuRootPressure - Class in etomica.normalmode
-
- DataSourceMuRoot.DataSourceMuRootVacancyConcentration - Class in etomica.normalmode
-
- DataSourceMuRoot1 - Class in etomica.normalmode
-
Datasource that returns an estimate of mu based on thermodynamic
self-consistency of pressure measurements and defect free energies.
- DataSourceMuRoot1(MCMoveOverlapListener, double, DataDistributer, double, double, double) - Constructor for class etomica.normalmode.DataSourceMuRoot1
-
- DataSourceMuRoot1.DataSourceMuRootPressure - Class in etomica.normalmode
-
- DataSourceMuRoot1.DataSourceMuRootVacancyConcentration - Class in etomica.normalmode
-
- DataSourceMuRootDPressure() - Constructor for class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootDPressure
-
- DataSourceMuRootDU() - Constructor for class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootDU
-
- DataSourceMuRootPMatch - Class in etomica.normalmode
-
Datasource that returns an estimate of mu based on thermodynamic
self-consistency of pressure measurements and defect free energies.
- DataSourceMuRootPMatch(MCMoveOverlapListener, double, DataDistributer, double, double, double) - Constructor for class etomica.normalmode.DataSourceMuRootPMatch
-
- DataSourceMuRootPMatch.DataSourceMuRootPressure - Class in etomica.normalmode
-
- DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration - Class in etomica.normalmode
-
- DataSourceMuRootPressure() - Constructor for class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootPressure
-
- DataSourceMuRootPressure() - Constructor for class etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootPressure
-
- DataSourceMuRootPressure() - Constructor for class etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootPressure
-
- DataSourceMuRootVacancyConcentration() - Constructor for class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootVacancyConcentration
-
- DataSourceMuRootVacancyConcentration() - Constructor for class etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootVacancyConcentration
-
- DataSourceMuRootVacancyConcentration() - Constructor for class etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration
-
- DataSourceOverlapAvgCollapsing() - Constructor for class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
-
- DataSourceOverlapAvgCollapsingSplit(DataSplitter) - Constructor for class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsingSplit
-
- DataSourceOverlapAvgSimple(AccumulatorAverage) - Constructor for class etomica.overlap.DataOverlap.DataSourceOverlapAvgSimple
-
- DataSourcePMu - Class in etomica.normalmode
-
DataSource that returns P2-P1 or mu-mu* as a function of mu.
- DataSourcePMu(MCMoveOverlapListener, double, int, double, DataDistributer, double, double, double, boolean) - Constructor for class etomica.normalmode.DataSourcePMu
-
- DataSourcePN - Class in etomica.normalmode
-
DataSource that returns measured pressure as a function of N
- DataSourcePN(DataDistributer, int) - Constructor for class etomica.normalmode.DataSourcePN
-
- DataSourcePoints - Class in etomica.data
-
- DataSourcePoints(String, Dimension, Dimension) - Constructor for class etomica.data.DataSourcePoints
-
- DataSourcePositioned - Interface in etomica.data
-
Interface for a DataSource that can return a value given an arbitrary
position.
- DataSourcePositionedBoltzmannFactor - Class in etomica.data
-
Calculates the Boltzmann factor at a position within a box a molecule of a
particular species would have if it existed at that point.
- DataSourcePositionedBoltzmannFactor(Space) - Constructor for class etomica.data.DataSourcePositionedBoltzmannFactor
-
- DataSourceProbabilityDensity - Class in etomica.modules.entropylottery
-
- DataSourceProbabilityDensity() - Constructor for class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- dataSourceRef - Variable in class etomica.overlap.MeterOverlap
-
- dataSourceRefBias - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- dataSourceRefFE - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- dataSourceRefStdev - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- DataSourceRmsVelocity - Class in etomica.data
-
Meter for the root-mean-square velocity of a set of atoms.
- DataSourceRmsVelocity() - Constructor for class etomica.data.DataSourceRmsVelocity
-
- DataSourceRmsVelocity(Histogram) - Constructor for class etomica.data.DataSourceRmsVelocity
-
- DataSourceScalar - Class in etomica.data
-
Particular data source for which the data is a simple scalar of type double.
- DataSourceScalar(String, Dimension) - Constructor for class etomica.data.DataSourceScalar
-
- dataSourceTarget - Variable in class etomica.overlap.MeterOverlap
-
- dataSourceTargetBias - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- dataSourceTargetFE - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- dataSourceTargetStdev - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- DataSourceTensorVirialHard - Class in etomica.data
-
A MeterTensor that returns the virial component of the pressure tensor for a hard potential.
- DataSourceTensorVirialHard(Space) - Constructor for class etomica.data.DataSourceTensorVirialHard
-
- DataSourceTensorVirialHard(Space, IntegratorHard) - Constructor for class etomica.data.DataSourceTensorVirialHard
-
- DataSourceTensorVirialHardProfile - Class in etomica.modules.interfacial
-
A DataSource that collects the average virial tensor as a function of
position for one dimension.
- DataSourceTensorVirialHardProfile(Space) - Constructor for class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- DataSourceTensorVirialHardProfile.DataSourceVirialProfile - Class in etomica.modules.interfacial
-
- DataSourceUa(DataOverlap) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa
-
- DataSourceUa2(IntegratorOverlap, DataOverlap, AccumulatorAverage, AccumulatorAverage) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
-
- DataSourceUniform - Class in etomica.data
-
A DataSource object that provides a set of uniformly spaced values between
two limits.
- DataSourceUniform() - Constructor for class etomica.data.DataSourceUniform
-
Default constructor.
- DataSourceUniform(String, Dimension) - Constructor for class etomica.data.DataSourceUniform
-
- DataSourceUniform(String, Dimension, int, double, double) - Constructor for class etomica.data.DataSourceUniform
-
Constructs a DataSourceUniform using the indicated number of values
and x range, and INCLUSIVE limits.
- DataSourceUniform(String, Dimension, int, double, double, DataSourceUniform.LimitType, DataSourceUniform.LimitType) - Constructor for class etomica.data.DataSourceUniform
-
Constructs a DataSourceUniform using the indicated number of values,
x range, and limit types, with dataInfo indicating that the data have
the given dimension.
- DataSourceUniform.LimitType - Enum in etomica.data
-
Typed constant that indicates the way limits of the range are interpreted.
- DataSourceVaporDensity(String, Dimension) - Constructor for class etomica.modules.droplet.DropletAtomicGraphic.DataSourceVaporDensity
-
- DataSourceVirialOverlap - Class in etomica.virial.overlap
-
Measures ratio of two cluster integrals using overlap sampling.
- DataSourceVirialOverlap(AccumulatorVirialOverlapSingleAverage, AccumulatorVirialOverlapSingleAverage) - Constructor for class etomica.virial.overlap.DataSourceVirialOverlap
-
- DataSourceVirialProfile(DataSourceTensorVirialHardProfile) - Constructor for class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
-
- DataSourceWallPressure - Class in etomica.modules.pistoncylinder
-
data source front for virial sum from P1HardMovingBoundary
returns pressure exerted on the wall by atoms
- DataSourceWallPressure(Space, P1HardMovingBoundary) - Constructor for class etomica.modules.pistoncylinder.DataSourceWallPressure
-
- DataSourceWallPressureCatalysis - Class in etomica.modules.catalysis
-
- DataSourceWallPressureCatalysis(Space, ISpecies, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- DataSourceWallPressureMu - Class in etomica.modules.mu
-
- DataSourceWallPressureMu(Space) - Constructor for class etomica.modules.mu.DataSourceWallPressureMu
-
- DataSplitter - Class in etomica.data
-
DataSink that takes a Data object and pushes each numerical value from the
incoming Data to a different stream.
- DataSplitter() - Constructor for class etomica.data.DataSplitter
-
- DataSplitter.IDataSinkFactory - Interface in etomica.data
-
- DataStreamAction - Class in etomica.data
-
- DataStreamAction() - Constructor for class etomica.data.DataStreamAction
-
- DataStreamResource - Class in etomica.server.resources.data
-
- DataStreamResource(SimulationStore, DataStreamStore, DataSourceIndex) - Constructor for class etomica.server.resources.data.DataStreamResource
-
- DataStreamStore - Class in etomica.server.dao
-
- DataStreamStore() - Constructor for class etomica.server.dao.DataStreamStore
-
- DataStreamStore.DataPlumbing - Class in etomica.server.dao
-
- DataStreamWebsocket - Class in etomica.server.resources.data
-
- DataStreamWebsocket(SimulationStore, DataStreamStore, ObjectMapper, ScheduledThreadPoolExecutor) - Constructor for class etomica.server.resources.data.DataStreamWebsocket
-
- DataStreamWebsocket.DataAndInfoEncoder - Class in etomica.server.resources.data
-
- DataTable - Class in etomica.data.types
-
Data object that holds double[] arrays as if they are columns in a
table.
- DataTable(int, int) - Constructor for class etomica.data.types.DataTable
-
Creates a new table with a specified number of columns all of a given
length.
- DataTable(DataDoubleArray[]) - Constructor for class etomica.data.types.DataTable
-
- dataTable - Variable in class etomica.graphics.DisplayTable
-
- DataTable.DataInfoTable - Class in etomica.data.types
-
- DataTable.DataInfoTableFactory - Class in etomica.data.types
-
- DataTableAverages - Class in etomica.data
-
Convenience class for a data table that collects the AccumulatorAverage
statistics for a collection of DataSource instances.
- DataTableAverages(Integrator) - Constructor for class etomica.data.DataTableAverages
-
Sets up table with default types that give the current value, the
average, and the error bars.
- DataTableAverages(Integrator, int, ArrayList<DataPump>) - Constructor for class etomica.data.DataTableAverages
-
- DataTableAverages(Integrator, AccumulatorAverage.StatType[], int, IDataSource[], ArrayList<DataPump>) - Constructor for class etomica.data.DataTableAverages
-
Sets up table with no sources.
- DataTableListener - Interface in etomica.data
-
Interface for a class that performs some action in response to
a change in a DataSinkTable instance.
- DataTableWriter - Class in etomica.data
-
A DataWriter that writes out data as a table with optional column headings
- DataTableWriter() - Constructor for class etomica.data.DataTableWriter
-
- DataTag - Class in etomica.data
-
Data stream identifier.
- DataTag() - Constructor for class etomica.data.DataTag
-
- DataTagBag - Class in etomica.graphics
-
Simple class that associates a set of tags with an object (unit, label, etc)
- DataTagBag(DataTag[], Object) - Constructor for class etomica.graphics.DataTagBag
-
- DataTensor - Class in etomica.data.types
-
Data object wrapping a single mutable value of type (Space) Tensor.
- DataTensor(Space) - Constructor for class etomica.data.types.DataTensor
-
Constructs a new instance with the given DataInfo, wrapping a new Tensor
instance from the given space.
- DataTensor.DataInfoTensor - Class in etomica.data.types
-
- DataTensor.DataInfoTensorFactory - Class in etomica.data.types
-
- dataTrueEy - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- dataVar - Variable in class etomica.modules.multiharmonic.DataProcessorVar
-
- DataVector - Class in etomica.data.types
-
Data object wrapping a single mutable value of type (Space) Vector.
- DataVector(Space) - Constructor for class etomica.data.types.DataVector
-
Constructs a new instance with the given DataInfo, wrapping a new Vector
instance from the given space.
- DataVector.DataInfoVector - Class in etomica.data.types
-
- DataVector.DataInfoVectorFactory - Class in etomica.data.types
-
- DataVirialOverlap - Class in etomica.virial.overlap
-
Convenience class that analyzes data from the reference and target system,
providing average and error estimates on values and ratios.
- DataVirialOverlap(AlphaSource, AccumulatorRatioAverageCovarianceFull, AccumulatorRatioAverageCovarianceFull) - Constructor for class etomica.virial.overlap.DataVirialOverlap
-
- DataVirialOverlap.FullResult - Class in etomica.virial.overlap
-
- dataWalkerAction(Object) - Method in class etomica.action.ResetAccumulators
-
- dataWalkerAction(Object) - Method in class etomica.action.ResetAccumulatorsAveraged
-
- dataWalkerAction(Object) - Method in class etomica.data.DataStreamAction
-
- DataWriter(int, DisplayPlot) - Constructor for class etomica.graphics.DisplayPlot.DataWriter
-
- dataWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- date - Static variable in class org.jmol.viewer.JmolConstants
-
- dbc - Variable in class etomica.dimer.P1LepsHarmonic
-
- DBDEN - Static variable in class etomica.math.Gamma
-
- DBNUM - Static variable in class etomica.math.Gamma
-
- DBO2C2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- DBO2H1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- dBOType - Variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- DC - Static variable in class etomica.math.Gamma
-
- dc11 - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- DCF - Class in etomica.virial.cluster
-
Main method that simply generates and displays the graphs in the direct
correlation function.
- DCF() - Constructor for class etomica.virial.cluster.DCF
-
- dcom - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- DCVGCMD - Class in etomica.modules.dcvgcmd
-
Dual-control-volume grand-canonical molecular dynamics simulation.
- DCVGCMD() - Constructor for class etomica.modules.dcvgcmd.DCVGCMD
-
- DCVGCMDGraphic - Class in etomica.modules.dcvgcmd
-
- DCVGCMDGraphic(DCVGCMD, Space) - Constructor for class etomica.modules.dcvgcmd.DCVGCMDGraphic
-
- DCVGCMDGraphic.Applet - Class in etomica.modules.dcvgcmd
-
- dd - Variable in class etomica.math.numerical.AkimaSplineSmootherApp.PlotAction
-
- dd - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp.PlotAction
-
- dd(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
-
- dd(int, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- dda - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- ddamp(int, double, double) - Method in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- dDimension() - Method in class etomica.units.dimensions.DimensionRatio
-
- ddP - Variable in class etomica.normalmode.MeterSolidProps
-
- ddP - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- DE(IData) - Method in interface etomica.data.IData
-
Divide-equals (/=) operation.
- DE(double) - Method in interface etomica.data.IData
-
Divide-equals (*=) operation, dividing all values in data by given
value.
- DE(IData) - Method in class etomica.data.types.DataDouble
-
Divide-equals (/=) operation.
- DE(double) - Method in class etomica.data.types.DataDouble
-
Divide-equals (/=) operation.
- DE(IData) - Method in class etomica.data.types.DataDoubleArray
-
Divide-equals (/=) operation.
- DE(double) - Method in class etomica.data.types.DataDoubleArray
-
Divide-equals (*=) operation.
- DE(IData) - Method in class etomica.data.types.DataDoubleBDArray
-
Divide-equals (/=) operation.
- DE(double) - Method in class etomica.data.types.DataDoubleBDArray
-
Times-equals (*=) operation.
- DE(IData) - Method in class etomica.data.types.DataGroup
-
- DE(double) - Method in class etomica.data.types.DataGroup
-
- DE(IData) - Method in class etomica.data.types.DataTensor
-
Divide-equals (/=) operation.
- DE(double) - Method in class etomica.data.types.DataTensor
-
Divide-equals (*=) operation.
- DE(IData) - Method in class etomica.data.types.DataVector
-
Divide-equals (/=) operation.
- DE(double) - Method in class etomica.data.types.DataVector
-
Divide-equals (*=) operation.
- DE(Tensor) - Method in interface etomica.space.Tensor
-
"Divide equals" (/=) operation, element-by-element.
- DE(Vector) - Method in interface etomica.space.Vector
-
Divide-equals (/=) operation.
- DE(Tensor) - Method in class etomica.space1d.Tensor1D
-
- DE(Vector) - Method in class etomica.space1d.Vector1D
-
- DE(Tensor) - Method in class etomica.space2d.Tensor2D
-
- DE(Vector) - Method in class etomica.space2d.Vector2D
-
- DE(Tensor) - Method in class etomica.space3d.Tensor3D
-
- DE(Vector) - Method in class etomica.space3d.Vector3D
-
- DE(Tensor) - Method in class etomica.spaceNd.TensorND
-
- DE(Vector) - Method in class etomica.spaceNd.VectorND
-
- DE(IBigValue) - Method in class etomica.veos.BigValue
-
Divide-equals (/=) operation.
- DE(IBigValue) - Method in interface etomica.veos.IBigValue
-
Divide-equals (/=) operation.
- DE(IBigValue) - Method in class etomica.veos.MyBigDecimal
-
Divide-equals (/=) operation.
- deactivate() - Method in class etomica.util.Grabber.ActionCornerSetter
-
- debug - Variable in class etomica.association.MCMoveMoleculeRotateAssociated
-
- debug - Variable in class etomica.models.co2.P2CO2Hellmann
-
- debug - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- debug - Static variable in class etomica.potential.PotentialCalculationEnergySum
-
- Debug - Class in etomica.util
-
Class holding static fields that determine whether debugging is on, how
much, what types and what (if anything) should be looked at specifically.
- Debug() - Constructor for class etomica.util.Debug
-
- debug - Static variable in class etomica.virial.ClusterSum
-
- debug - Static variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- debug - Variable in class etomica.virial.ClusterWheatleySoft
-
- debug - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- debug - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- debug - Static variable in class etomica.virial.MayerGeneral
-
- debug - Static variable in class org.jmol.script.Token
-
- debug(String) - Method in class org.jmol.util.DefaultLogger
-
- debug(String) - Static method in class org.jmol.util.Logger
-
Writes a log at DEBUG level.
- debug(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at DEBUG level.
- DEBUG_MODE - Static variable in class etomica.graph.engine.impl.ParserImpl
-
- DEBUG_MODE - Static variable in class etomica.graph.iterators.filters.IsomorphismFilter
-
- DEBUG_NOW - Static variable in class etomica.util.Debug
-
true if debugging is currently enabled (when the integrator reaches step START)
- debugging - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- debugging - Static variable in class org.jmol.util.Logger
-
- debuggingHigh - Static variable in class org.jmol.util.Logger
-
- debugme - Static variable in class etomica.models.co2.PNCO2GCPM
-
- debugme - Static variable in class etomica.models.co2.PNGCPM
-
- debugMoleculePair - Static variable in class etomica.util.Debug
-
- debugPair - Static variable in class etomica.util.Debug
-
- debugscript - Static variable in class org.jmol.script.Token
-
- Debye - Class in etomica.units
-
The debye unit of electrical dipole moment, equal to 10^-18 statC-cm,
or 3.33564e-30 C-m.
- dec() - Method in interface etomica.graph.model.Bitmap
-
Decrements the integer value of this bitmap by one: bitmap--.
- dec() - Method in class etomica.graph.model.impl.AbstractBitmap
-
- decapitalize(String) - Static method in class etomica.util.Strings
-
Converts the first letter of the given string to lower case.
- Decimal - Class in etomica.units
-
Decimal representation of something that represents the fractional
amount of a whole (e.g., mole fraction) as a decimal value typically
between 0 and 1.
- decimal - Static variable in class org.jmol.script.Token
-
- DecimalSlider - Class in etomica.graphics
-
Slider that permits variation of decimal (non-integer) values.
- DecimalSlider() - Constructor for class etomica.graphics.DecimalSlider
-
- Decorate - Class in etomica.graph.operations
-
Performs decoration of diagrams by points.
- Decorate() - Constructor for class etomica.graph.operations.Decorate
-
- Decorate.DecorateParameters - Class in etomica.graph.operations
-
- DecorateNaphthalene2Site(MulFlexible.MulFlexibleParameters, char, char, char, char, Set<Graph>, Set<Graph>, Set<Graph>) - Constructor for class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- DecorateParameters(char, MulFlexible.MulFlexibleParameters) - Constructor for class etomica.graph.operations.Decorate.DecorateParameters
-
- DecorateParameters(int, MulFlexible.MulFlexibleParameters) - Constructor for class etomica.graph.operations.Decorate.DecorateParameters
-
- DecorateWertheim2Site - Class in etomica.graph.operations
-
Performs decoration of diagrams by various density points.
- DecorateWertheim2Site() - Constructor for class etomica.graph.operations.DecorateWertheim2Site
-
- DecorateWertheim2Site.DecorateWertheimParameters2Site - Class in etomica.graph.operations
-
- DecorateWertheim2SiteRho - Class in etomica.graph.operations
-
Performs decoration of diagrams by various density points.
- DecorateWertheim2SiteRho() - Constructor for class etomica.graph.operations.DecorateWertheim2SiteRho
-
- DecorateWertheim2SiteRho.DecorateWertheimParameters2Site - Class in etomica.graph.operations
-
- DecorateWertheim3SiteRho - Class in etomica.graph.operations
-
Performs decoration of diagrams by various density points.
- DecorateWertheim3SiteRho() - Constructor for class etomica.graph.operations.DecorateWertheim3SiteRho
-
- DecorateWertheim3SiteRho.DecorateWertheimParameters3Site - Class in etomica.graph.operations
-
- DecorateWertheimNaphthalene2Rho - Class in etomica.graph.operations
-
modified from Hye Min's DecorateWertheim2SiteRho class
Performs decoration of diagrams by various density points.
- DecorateWertheimNaphthalene2Rho() - Constructor for class etomica.graph.operations.DecorateWertheimNaphthalene2Rho
-
- DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site - Class in etomica.graph.operations
-
- DecorateWertheimParameters2Site(int, MulFlexible.MulFlexibleParameters, char, char, Set<Graph>, Set<Graph>, Set<Graph>) - Constructor for class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
-
- DecorateWertheimParameters2Site(MulFlexible.MulFlexibleParameters, char, char, Set<Graph>, Set<Graph>, Set<Graph>) - Constructor for class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
-
- DecorateWertheimParameters3Site(MulFlexible.MulFlexibleParameters, char, char, char, char, char, char, char, char, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>, Set<Graph>) - Constructor for class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- decrementCollisionTime(double) - Method in class etomica.integrator.IntegratorHard.Agent
-
Decreases the recorded time to collision of this atom
This action is performed when the atom is advanced without a collision
- def - Variable in class etomica.modules.droplet.EllipseDisplayAction
-
- DEF_ISOMORPHISM_ALGO - Static variable in class etomica.graph.isomorphism.Match
-
- DEFAULT_ATOM_COLOR - Static variable in class etomica.graphics.ColorScheme
-
- DEFAULT_BOND_MILLIANGSTROM_RADIUS - Static variable in class org.jmol.viewer.JmolConstants
-
- DEFAULT_BOND_RADIUS - Static variable in class org.jmol.viewer.JmolConstants
-
- DEFAULT_BOND_TOLERANCE - Static variable in class org.jmol.viewer.JmolConstants
-
- DEFAULT_FONTFACE - Static variable in class org.jmol.viewer.JmolConstants
-
- DEFAULT_FONTSTYLE - Static variable in class org.jmol.viewer.JmolConstants
-
- DEFAULT_HEIGHT - Static variable in class etomica.graph.view.rasterizer.SVGConverter
-
Default height
- DEFAULT_HELP_PATH - Static variable in class org.jmol.viewer.JmolConstants
-
- DEFAULT_MAX_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
-
- DEFAULT_MAX_TEMPERATURE - Static variable in class etomica.graphics.DeviceThermoSlider
-
- DEFAULT_MIN_BOND_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
-
- DEFAULT_MIN_CONNECT_DISTANCE - Static variable in class org.jmol.viewer.JmolConstants
-
- DEFAULT_MIN_TEMPERATURE - Static variable in class etomica.graphics.DeviceThermoSlider
-
- DEFAULT_PERCENT_VDW_ATOM - Static variable in class org.jmol.viewer.JmolConstants
-
- DEFAULT_QUALITY - Static variable in class etomica.graph.view.rasterizer.SVGConverter
-
Default quality value.
- DEFAULT_RESULT_TYPE - Static variable in class etomica.graph.view.rasterizer.SVGConverter
-
Default result type
- DEFAULT_SIZE - Static variable in class etomica.modules.crystalviewer.LatticeEditor
-
- DEFAULT_STEREO_DEGREES - Static variable in enum org.jmol.constant.EnumStereoMode
-
- DEFAULT_STRUT_RADIUS - Static variable in class org.jmol.viewer.JmolConstants
-
- DEFAULT_WIDTH - Static variable in class etomica.graph.view.rasterizer.SVGConverter
-
Default width
- defaultAdjustInterval - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
-
- defaultAdjustStep - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
-
- defaultanglelabel - Static variable in class org.jmol.script.Token
-
- defaultColor - Variable in class etomica.graphics.ColorScheme
-
- defaultcolorscheme - Static variable in class org.jmol.script.Token
-
- defaultColorsUsed - Variable in class etomica.graphics.ColorSchemeByType
-
- defaultdirectory - Static variable in class org.jmol.script.Token
-
- defaultdistancelabel - Static variable in class org.jmol.script.Token
-
- defaultdrawarrowscale - Static variable in class org.jmol.script.Token
-
- defaultdropscript - Static variable in class org.jmol.script.Token
-
- defaultFileName() - Method in class etomica.data.DataLogger
-
- defaultFontFamily - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Default value for the font-family when it is unspecified
- defaultIOUnit() - Method in class etomica.data.DataSourceAcceptanceProbability
-
- defaultIOUnit() - Method in class etomica.data.DataSourceAcceptanceRatio
-
- DefaultIterator - Class in etomica.graph.iterators
-
- DefaultIterator(byte) - Constructor for class etomica.graph.iterators.DefaultIterator
-
- DefaultIterator(byte, byte) - Constructor for class etomica.graph.iterators.DefaultIterator
-
- defaultlabelpdb - Static variable in class org.jmol.script.Token
-
- defaultlabelxyz - Static variable in class org.jmol.script.Token
-
- defaultlattice - Static variable in class org.jmol.script.Token
-
- defaultloadfilter - Static variable in class org.jmol.script.Token
-
- defaultloadscript - Static variable in class org.jmol.script.Token
-
- DefaultLogger - Class in org.jmol.util
-
Default implementation of the logger.
- DefaultLogger() - Constructor for class org.jmol.util.DefaultLogger
-
- defaultMouseListener - Variable in class etomica.util.Grabber
-
- DefaultMouseListener(Grabber) - Constructor for class etomica.util.Grabber.DefaultMouseListener
-
- DefaultPermutator - Class in etomica.graph.iterators
-
- DefaultPermutator(int[]) - Constructor for class etomica.graph.iterators.DefaultPermutator
-
- defaults - Static variable in class org.jmol.script.Token
-
- defaultstructuredssp - Static variable in class org.jmol.script.Token
-
- DefaultSVGConverterController - Class in etomica.graph.view.rasterizer
-
Default controller for the
SVGConverter operation.
- DefaultSVGConverterController() - Constructor for class etomica.graph.view.rasterizer.DefaultSVGConverterController
-
- DefaultToolbar - Class in etomica.graphics
-
- DefaultToolbar() - Constructor for class etomica.graphics.DefaultToolbar
-
- DefaultToolbar(JPanel, String) - Constructor for class etomica.graphics.DefaultToolbar
-
- defaulttorsionlabel - Static variable in class org.jmol.script.Token
-
- defaulttranslucent - Static variable in class org.jmol.script.Token
-
- defaultValue() - Method in enum etomica.virial.GUI.models.EnumPotentialParamDescription
-
- defaultvdw - Static variable in class org.jmol.script.Token
-
- defBit(int, boolean) - Method in interface etomica.graph.model.Bitmap
-
- defBit(int, boolean) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- defdfmt - Static variable in class etomica.util.ScientificFormat
-
- defefmt - Static variable in class etomica.util.ScientificFormat
-
- define - Static variable in class org.jmol.script.Token
-
- deform(Tensor) - Method in class etomica.space.BoundaryDeformablePeriodic
-
Applies the given deformation tensor to the boundary in its current
shape.
- deformation - Variable in class etomica.modules.droplet.ConfigurationDroplet
-
- Degree - Class in etomica.units
-
Standard degree angular unit, such that for example a right angle is 90 degrees.
- degree() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Polynomial degree.
- degree - Variable in class etomica.virial.MCMoveClusterAtomHSTree
-
- degree - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
-
- del_r - Variable in class etomica.virial.CalcFFT
-
- delayExponent - Variable in class etomica.graphics.DeviceDelaySlider
-
- delaymaximumms - Static variable in class org.jmol.script.Token
-
- Delete - Class in etomica.graph.operations
-
- Delete() - Constructor for class etomica.graph.operations.Delete
-
- delete(int) - Method in class etomica.modules.render.ParseObj
-
Removes the vertex referenced by the given index from the list of vertices,
removes its bonds from the list of bonds, shifts all vertex indexes down
to fill its slot, and returns a list of indexes (after shifting) of vertices
that were bonded to the given vertex.
- delete - Static variable in class org.jmol.script.Token
-
- deleteBits(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
-
this one slides deleted bits out of a pattern.
- deleteCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- deleteCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- deleteCandidateSet - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- deleteCandidateTimes - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- deleteCandidateTimes - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- deleteConnection(int, int) - Method in class etomica.virial.cluster.ClusterDiagram
-
Deletes a connection from one node1 to node2.
- deleteEdge(byte) - Method in interface etomica.graph.model.Graph
-
- deleteEdge(byte, byte) - Method in interface etomica.graph.model.Graph
-
- deleteEdge(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- deleteEdge(byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- DeleteEdge - Class in etomica.graph.operations
-
Deletes all edges of a given color.
- DeleteEdge() - Constructor for class etomica.graph.operations.DeleteEdge
-
- DeleteEdgeParameters - Class in etomica.graph.operations
-
- DeleteEdgeParameters(char) - Constructor for class etomica.graph.operations.DeleteEdgeParameters
-
- deleteElements(Object, int, int) - Static method in class org.jmol.util.ArrayUtil
-
- deleteInstance(String) - Method in class etomica.server.resources.SimulationResource
-
- deleteRow(int) - Method in class etomica.graphics.DeviceTableModelGeneric
-
Delete an entire row from the table
- delta - Variable in class etomica.action.IntegratorDimerApproach
-
- delta - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- delta1 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- delta1 - Variable in class etomica.normalmode.MCMoveSingleMode
-
- delta2 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- delta2 - Variable in class etomica.normalmode.MCMoveSingleMode
-
- deltaA(double, double, int) - Method in class etomica.statmech.HardSphere
-
Returns the difference between absolute free energies between the given
densities for solid (FCC) hard spheres.
- deltaBMu - Variable in class etomica.normalmode.DataSourcePMu
-
- deltaCut2 - Variable in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizable
-
- deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- deltaCut2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- deltaEps - Variable in class etomica.potential.P2PenetrableSquareWell
-
- deltaMu - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- deltaP - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- deltaR - Variable in class etomica.dimer.IntegratorDimerMin
-
- deltaR - Variable in class etomica.dimer.IntegratorDimerRT
-
- deltaTheta - Variable in class etomica.dimer.IntegratorDimerMin
-
- deltaTheta - Variable in class etomica.dimer.IntegratorDimerRT
-
- deltaU - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- deltaU - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- deltaU - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- deltaU - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- deltaU - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- deltaU - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- deltaU - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- deltaU - Variable in class etomica.normalmode.MCMoveSingleMode
-
- deltaV - Variable in class etomica.dimer.IntegratorDimerRT
-
- deltaV - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- deltaX - Variable in class etomica.action.BoxInflateAnisotropic
-
- deltaX - Variable in class etomica.data.histogram.HistogramNotSoSimple
-
- deltaX - Variable in class etomica.data.histogram.HistogramReweightedData
-
- deltaX - Variable in class etomica.data.histogram.HistogramSimple
-
- deltaXl - Variable in class etomica.dimer.IntegratorDimerRT
-
- deltaXmax - Variable in class etomica.dimer.IntegratorDimerRT
-
- DemoSim - Class in etomica.simulation.prototypes
-
A demo simulation to test aspects of the frontend.
- DemoSim() - Constructor for class etomica.simulation.prototypes.DemoSim
-
- denom() - Method in class etomica.veos.bigdecimal.Rational
-
Get the denominator.
- denominator - Variable in class etomica.math.Rational
-
- denominator() - Method in class etomica.math.Rational
-
Returns the denominator.
- denomSum - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- denomSum - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- denomSum - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
-
- denomSum - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- denomSum - Variable in class etomica.normalmode.MeterWorkTargetBennet
-
- denomSum - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- denomSum - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- denomSum - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- dense - Variable in class etomica.potential.P2QChemInterpolated
-
- density - Variable in class etomica.AlkaneEH.CH4NVT.Param
-
- density - Variable in class etomica.AlkaneEH.DHS_NVT.Param
-
- density - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- density - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
-
- density - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- density - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- density - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- density - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
-
- density - Variable in class etomica.dielectric.DHS_NVT.Param
-
- density - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- density - Variable in class etomica.dielectric.TIP4P_NVT.Param
-
- density - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- density - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
-
- density - Variable in class etomica.freeenergy.npath.SimLattice.LjMC3DParams
-
- density - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
-
- density - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
-
- density - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- density - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- density - Variable in class etomica.mappedRdf.MappedRdf.LJMDParams
-
- density - Variable in class etomica.mappedvirial.MappedU.LJMDParams
-
- density - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
-
- density - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
-
- density - Variable in class etomica.meam.EFSTungsten.Params
-
- density - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- density - Variable in class etomica.metastable.LJNVT.LJMCParams
-
- density - Variable in class etomica.models.nitrogen.FindTransitionTemperature
-
- density - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- density - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- density - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- density - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- density - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- density - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- density - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
-
- density - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- density - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
-
- density - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- density - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- density - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- density - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- density - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- density - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- density - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
-
- density - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- density - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
-
- density - Variable in class etomica.modules.droplet.DropletAtomic
-
- density - Variable in class etomica.modules.render.RenderMD.RenderMDParam
-
- density - Variable in class etomica.modules.vle.MCMoveMoleculeExchangeVLE
-
- density - Variable in class etomica.modules.vle.MCMoveVolumeExchangeVLE
-
- density - Variable in class etomica.modules.vle.VLESim
-
- density - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
-
- density - Variable in class etomica.normalmode.MeterSolidProps
-
- density - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- density - Variable in class etomica.normalmode.MinimizeHCP
-
- density - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
-
- density - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- density - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- density - Variable in class etomica.normalmode.SimBennet.SimBennetParam
-
- density - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
-
- density - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
-
- density - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- density - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
-
- density - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
-
- density - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
-
- density - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
-
- density - Variable in class etomica.statmech.HardSphereSolid.EOSParams
-
- density - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- density1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- density2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- densityAccum - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
-
- densityBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- densityDisplay - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
-
- densityDisplayTextBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- densityForMu(double) - Static method in class etomica.statmech.HardSphereSolid
-
- densityForPressure(double) - Static method in class etomica.statmech.HardSphereSolid
-
- densityMeter - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- DensityOfState - Class in etomica.densityofstate
-
A Yukawa Monte-Carlo simulation in 3D
- DensityOfState() - Constructor for class etomica.densityofstate.DensityOfState
-
- DensityOfState(int) - Constructor for class etomica.densityofstate.DensityOfState
-
- DensityOfStatesPolynomial - Class in etomica.densityofstate
-
A Yukawa Monte-Carlo simulation in 3D
- DensityOfStatesPolynomial() - Constructor for class etomica.densityofstate.DensityOfStatesPolynomial
-
- DensityOfStatesPolynomial(int) - Constructor for class etomica.densityofstate.DensityOfStatesPolynomial
-
- densityProfileMeter - Variable in class etomica.modules.colloid.ColloidGraphic
-
- densityProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- densityProfileMeter - Variable in class etomica.surfacetension.SurfaceTensionMapped
-
- densityProfileMeterA - Variable in class etomica.modules.adsorption.AdsorptionGraphic
-
- densityProfileMeterB - Variable in class etomica.modules.adsorption.AdsorptionGraphic
-
- densityProfileSource - Variable in class etomica.data.DataProcessorChemicalPotential
-
- depth - Static variable in class org.jmol.script.Token
-
- depth - Variable in class org.jmol.util.GData
-
- DepthFirst - Class in etomica.graph.traversal
-
- DepthFirst() - Constructor for class etomica.graph.traversal.DepthFirst
-
- depthValue - Variable in class g3dsys.control.TransformManager
-
- derivative2nd(Vector, Potential2SoftSpherical) - Method in class etomica.normalmode.HessianDB
-
- DerivativeEnergyFunction - Class in etomica.conjugategradient
-
- DerivativeEnergyFunction(Box, PotentialMaster, Space) - Constructor for class etomica.conjugategradient.DerivativeEnergyFunction
-
- DerivativeEnergyFunction.MyAgentSource - Class in etomica.conjugategradient
-
- derivativeFunction - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- derive() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
First derivative.
- description() - Method in enum etomica.virial.GUI.models.EnumPotentialParamDescription
-
- desiredPressure - Variable in class etomica.models.nitrogen.FindTransitionTemperature
-
- dest - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- dest - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- dest - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- dest - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- destination - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- destination - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- DestinationType - Class in etomica.graph.view.rasterizer
-
Describes the type of destination for an SVGConverter operation.
- destinationType - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Result type
- destroy() - Method in class etomica.server.resources.ConfigurationWebsocket.ConfigurationUpdateEncoder
-
- destroy() - Method in class etomica.server.resources.data.DataStreamWebsocket.DataAndInfoEncoder
-
- destroy() - Method in class org.jmol.g3d.Graphics3D
-
- destroy() - Method in class org.jmol.util.GData
-
- det(BigInteger[][]) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Determinant of an integer square matrix.
- determinant() - Method in interface etomica.space.Tensor
-
Computes the determinant of the matrix represented by this tensor
- determinant() - Method in class etomica.space1d.Tensor1D
-
- determinant() - Method in class etomica.space2d.Tensor2D
-
- determinant() - Method in class etomica.space3d.Tensor3D
-
- determinant() - Method in class etomica.spaceNd.TensorND
-
- determinant() - Method in class org.jmol.util.Matrix3f
-
Computes the determinant of this matrix.
- determinant() - Method in class org.jmol.util.Matrix4f
-
Computes the determinant of this matrix.
- deviationVector - Variable in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
-
- Device - Class in etomica.graphics
-
Base class for all Devices.
- Device() - Constructor for class etomica.graphics.Device
-
- Device(Controller) - Constructor for class etomica.graphics.Device
-
- Device.ActionSet - Class in etomica.graphics
-
- DeviceBox - Class in etomica.graphics
-
A simple device the permits editing of a single value via a textbox
with an associated label.
- DeviceBox() - Constructor for class etomica.graphics.DeviceBox
-
- DeviceBox.LabelType - Enum in etomica.graphics
-
Typed constant used to indicate the type of label to be used with the display.
- deviceBoxValueChanged(DeviceBoxValueChangedEvent) - Method in class etomica.graphics.DeviceBox
-
- deviceBoxValueChanged(DeviceBoxValueChangedEvent) - Method in interface etomica.graphics.DeviceBoxValueChangedListener
-
- DeviceBoxValueChangedEvent - Class in etomica.graphics
-
- DeviceBoxValueChangedEvent(DeviceBox, int) - Constructor for class etomica.graphics.DeviceBoxValueChangedEvent
-
- DeviceBoxValueChangedListener - Interface in etomica.graphics
-
Interface that should be implemented to receive a value changed event
when a DeviceBox updateValue method is called.
- DeviceButton - Class in etomica.graphics
-
Button that causes an action to be performed.
- DeviceButton(Controller) - Constructor for class etomica.graphics.DeviceButton
-
Constructs button that is not connected to any action.
- DeviceButton(Controller, IAction) - Constructor for class etomica.graphics.DeviceButton
-
Constructs a button connected to the given action.
- DeviceButtonGroup - Class in etomica.graphics
-
Add etomica device for a group of radio buttons.
- DeviceButtonGroup(Controller, int) - Constructor for class etomica.graphics.DeviceButtonGroup
-
- DeviceButtonSingle - Class in etomica.zeolite
-
Button that causes an action to be performed.
- DeviceButtonSingle(Controller) - Constructor for class etomica.zeolite.DeviceButtonSingle
-
Constructs button that is not connected to any action.
- DeviceButtonSingle(Controller, IAction) - Constructor for class etomica.zeolite.DeviceButtonSingle
-
Constructs a button connected to the given action.
- DeviceCellNum3DSlider - Class in etomica.normalmode
-
- DeviceCellNum3DSlider(Controller) - Constructor for class etomica.normalmode.DeviceCellNum3DSlider
-
- DeviceCellNumXYSlider - Class in etomica.normalmode
-
- DeviceCellNumXYSlider(Controller) - Constructor for class etomica.normalmode.DeviceCellNumXYSlider
-
- DeviceCheckBox - Class in etomica.graphics
-
Button that toggles a boolean value via a check box.
- DeviceCheckBox(ModifierBoolean) - Constructor for class etomica.graphics.DeviceCheckBox
-
- DeviceCheckBox(String, ModifierBoolean) - Constructor for class etomica.graphics.DeviceCheckBox
-
- DeviceControllerButton - Class in etomica.graphics
-
Button that attaches to a controller to toggle its pause/resume state.
- DeviceControllerButton(Controller) - Constructor for class etomica.graphics.DeviceControllerButton
-
- DeviceDelaySlider - Class in etomica.graphics
-
- DeviceDelaySlider(Controller, ActivityIntegrate) - Constructor for class etomica.graphics.DeviceDelaySlider
-
- DeviceEigenvaluesSlider - Class in etomica.normalmode
-
- DeviceEigenvaluesSlider(Controller) - Constructor for class etomica.normalmode.DeviceEigenvaluesSlider
-
- deviceList() - Method in class etomica.graphics.SimulationGraphic
-
- DeviceNSelector - Class in etomica.graphics
-
Slider that selects the number of atoms of a given species in a box.
- DeviceNSelector() - Constructor for class etomica.graphics.DeviceNSelector
-
- DeviceNSelector(Controller) - Constructor for class etomica.graphics.DeviceNSelector
-
- DevicePlotPoints - Class in etomica.graphics
-
- DevicePlotPoints(IFunction[], String[], String[]) - Constructor for class etomica.graphics.DevicePlotPoints
-
- DevicePlotPoints(String[], IFunction[], String[], boolean) - Constructor for class etomica.graphics.DevicePlotPoints
-
- DeviceSelector - Class in etomica.graphics
-
Generic Device that has a combo box.
- DeviceSelector(Controller) - Constructor for class etomica.graphics.DeviceSelector
-
- DeviceSlider - Class in etomica.graphics
-
Device the changes a property using a graphical slider, via a Modifier.
- DeviceSlider(Controller) - Constructor for class etomica.graphics.DeviceSlider
-
- DeviceSlider(Controller, Object, String) - Constructor for class etomica.graphics.DeviceSlider
-
Constructs a slider connected to the given property of the given object
- DeviceSlider(Controller, Modifier) - Constructor for class etomica.graphics.DeviceSlider
-
Constructs a slider connected to the get/set Value methods of the given Modifier
- DeviceSpinner - Class in etomica.graphics
-
Device the changes a property using a graphical spinner, via a Modifier.
- DeviceSpinner(Controller) - Constructor for class etomica.graphics.DeviceSpinner
-
- DeviceSpinner(Controller, Object, String) - Constructor for class etomica.graphics.DeviceSpinner
-
Constructs a spinner connected to the given property of the given object
- DeviceSpinner(Controller, Modifier) - Constructor for class etomica.graphics.DeviceSpinner
-
Constructs a spinner connected to the get/set Value methods of the given Modifier
- DeviceSpinner.SpinnerListener - Class in etomica.graphics
-
Spinner listener, which relays the spinner change events to the modifier
- DeviceTable - Class in etomica.graphics
-
Presents a table of numeric properties that can be edited by typing in values.
- DeviceTable(String[]) - Constructor for class etomica.graphics.DeviceTable
-
- DeviceTable(TableModel) - Constructor for class etomica.graphics.DeviceTable
-
- DeviceTableModelGeneric - Class in etomica.graphics
-
- DeviceTableModelGeneric(Object[][], String[]) - Constructor for class etomica.graphics.DeviceTableModelGeneric
-
- DeviceThermoSelector - Class in etomica.graphics
-
Permits selection of temperature from a discrete set of values.
- DeviceThermoSelector(Simulation, IntegratorBox) - Constructor for class etomica.graphics.DeviceThermoSelector
-
Constructor that specifies Kelvin as temperature units.
- DeviceThermoSelector(Controller, Unit, boolean) - Constructor for class etomica.graphics.DeviceThermoSelector
-
- DeviceThermoSlider - Class in etomica.graphics
-
- DeviceThermoSlider(Controller, IntegratorBox) - Constructor for class etomica.graphics.DeviceThermoSlider
-
- DeviceThermoSliderGEMC - Class in etomica.modules.vle
-
Custom temperature slider for GEMC simulations.
- DeviceThermoSliderGEMC(Controller) - Constructor for class etomica.modules.vle.DeviceThermoSliderGEMC
-
- DeviceToggleButton - Class in etomica.graphics
-
Button that toggles a boolean value.
- DeviceToggleButton(Controller) - Constructor for class etomica.graphics.DeviceToggleButton
-
- DeviceToggleButton(Controller, ModifierBoolean) - Constructor for class etomica.graphics.DeviceToggleButton
-
- DeviceToggleButton(Controller, ModifierBoolean, String, String) - Constructor for class etomica.graphics.DeviceToggleButton
-
- DeviceToggleRadioButtons - Class in etomica.graphics
-
Button that toggles a boolean value using a pair of radio buttons.
- DeviceToggleRadioButtons(ModifierBoolean) - Constructor for class etomica.graphics.DeviceToggleRadioButtons
-
Constructor with default labels of a blank title and "True" and "False" for
the true/false labels.
- DeviceToggleRadioButtons(ModifierBoolean, String, String, String) - Constructor for class etomica.graphics.DeviceToggleRadioButtons
-
- DeviceTrioControllerButton - Class in etomica.graphics
-
Device comprising three buttons: (1) attaches to a controller to toggle its pause/resume state;
(2)causes a reset (restart) action of simulation to be performed; (3) causes reset of meter averages
only.
- DeviceTrioControllerButton(Simulation, Space, Controller) - Constructor for class etomica.graphics.DeviceTrioControllerButton
-
Contructs device with buttons that affect the given simulation.
- DeviceTrioControllerButton() - Constructor for class etomica.graphics.DeviceTrioControllerButton
-
No-argument contructor gives device that performs no action until
setSimulation is used to specify the target simulation.
- DeviceTrioControllerButton.ComponentEventControllerButton - Class in etomica.graphics
-
Inner class that catches action of simulation panel
- DeviceWaveVectorSlider - Class in etomica.normalmode
-
- DeviceWaveVectorSlider(Controller) - Constructor for class etomica.normalmode.DeviceWaveVectorSlider
-
- df(int[], double[]) - Method in class etomica.conjugategradient.DerivativeEnergyFunction
-
- df(int[], double[]) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- df(int[], double[]) - Method in class etomica.conjugategradient.TestNonLinearConjugateGradients
-
- df - Variable in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- df(int, double) - Method in class etomica.math.function.Function.Abs
-
- df(int, double) - Method in class etomica.math.function.Function.Constant
-
- df(int, double) - Method in class etomica.math.function.Function.Exp
-
- df(int, double) - Method in class etomica.math.function.Function.Identity
-
- df(int, double) - Method in class etomica.math.function.Function.Linear
-
- df(int, double) - Method in class etomica.math.function.Function.Log
-
- df(int, double) - Method in class etomica.math.function.Function.Reciprocal
-
- df(int, double) - Method in class etomica.math.function.Function.Sqrt
-
- df(int, double) - Method in class etomica.math.function.FunctionChain
-
Evaluates derivative via the chain rule.
- df(int, double) - Method in interface etomica.math.function.FunctionDifferentiable
-
- df(int[], double[]) - Method in interface etomica.math.function.FunctionMultiDimensionalDifferentiable
-
Returns the derivative indicated by the array d evaluated at the given point x.
- df(int[], double[]) - Method in class etomica.math.numerical.CalcGradientDifferentiable
-
- df(int[], double[]) - Method in class etomica.math.numerical.FiniteDifferenceDerivative
-
- df(int, double[], double) - Method in class etomica.math.numerical.FittingFunctionNonLinear
-
- df(int[], int, double[]) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- df(int, double) - Method in class etomica.modules.statistics.StatisticsMCGraphic.MyFunctionInvertible
-
- df(int[], double[]) - Method in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- df(int[], double[]) - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
-
- df2(int[], double[]) - Method in class etomica.math.numerical.CalcGradientDifferentiable
-
Uses the potential's force calculation at different displacements of a molecule in X, Y and Z
to determine the second derivative of the potential.
- dfdx(double) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
-
- dfmt - Variable in class etomica.util.ScientificFormat
-
- dForces - Variable in class etomica.dimer.SimDimerLJadatom
-
- dForces - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- dForces - Variable in class etomica.dimer.SimDimerMEAMGB
-
- dForces - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- dFrot - Variable in class etomica.dimer.IntegratorDimerMin
-
- dFrot - Variable in class etomica.dimer.IntegratorDimerRT
-
- dFsq - Variable in class etomica.dimer.IntegratorDimerRT
-
- DHS_NVT - Class in etomica.AlkaneEH
-
Canonical ensemble Monte Carlo simulation (NVT)
calculate dielectric constant for dipolar HS model
- DHS_NVT(Space, int, double, double, double, double, double, double) - Constructor for class etomica.AlkaneEH.DHS_NVT
-
- DHS_NVT - Class in etomica.dielectric
-
Canonical ensemble Monte Carlo simulation (NVT)
calculate dielectric constant for dipolar HS model
Electric field mapped average for dielectric constant
- DHS_NVT(Space, int, double, double, double, double, double, double) - Constructor for class etomica.dielectric.DHS_NVT
-
- DHS_NVT.DipoleSourceDHS - Class in etomica.AlkaneEH
-
- DHS_NVT.DipoleSourceDHS - Class in etomica.dielectric
-
- DHS_NVT.Param - Class in etomica.AlkaneEH
-
- DHS_NVT.Param - Class in etomica.dielectric
-
- dHSCore - Static variable in class etomica.potential.P2NitrogenHellmann
-
- diagE(Vector) - Method in interface etomica.space.Tensor
-
Makes this a diagonal tensor with elements set by the given vector.
- diagE(Vector) - Method in class etomica.space1d.Tensor1D
-
- diagE(Vector) - Method in class etomica.space2d.Tensor2D
-
- diagE(Vector) - Method in class etomica.space3d.Tensor3D
-
- diagE(Vector) - Method in class etomica.spaceNd.TensorND
-
- diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- diagramIndex - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- diagramIndex - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- diagramIndex - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
-
- diagramIndex - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
-
- DiagramSource - Interface in etomica.virial.cluster
-
- diameter - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedSite
-
- DiameterHash - Interface in etomica.atom
-
This provides an interface for a class that acts like a hashmap for atomic
diameters.
- diameterHash - Variable in class etomica.graphics.DisplayBox
-
- diameterHash - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- diameterHash - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- DiameterHashByElement - Class in etomica.atom
-
This class hashes atomic diameters based on the element.
- DiameterHashByElement() - Constructor for class etomica.atom.DiameterHashByElement
-
- DiameterHashByElementType - Class in etomica.atom
-
This class hashes atomic diameters based on both element and atom type.
- DiameterHashByElementType() - Constructor for class etomica.atom.DiameterHashByElementType
-
- DiameterHashByType - Class in etomica.atom
-
This class hashes atomic diameters based on the atom type.
- DiameterHashByType() - Constructor for class etomica.atom.DiameterHashByType
-
- dielectricOutside - Variable in class etomica.AlkaneEH.DHS_NVT.Param
-
- dielectricOutside - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- dielectricOutside - Variable in class etomica.dielectric.DHS_NVT.Param
-
- dielectricOutside - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- dielectricOutside - Variable in class etomica.dielectric.TIP4P_NVT.Param
-
- DifByConstant - Class in etomica.graph.operations
-
- DifByConstant() - Constructor for class etomica.graph.operations.DifByConstant
-
- DifByConstant.DifByConstantParameters - Class in etomica.graph.operations
-
- DifByConstantParameters(char, char) - Constructor for class etomica.graph.operations.DifByConstant.DifByConstantParameters
-
- DifByEdge - Class in etomica.graph.operations
-
- DifByEdge() - Constructor for class etomica.graph.operations.DifByEdge
-
- DifByNode - Class in etomica.graph.operations
-
- DifByNode() - Constructor for class etomica.graph.operations.DifByNode
-
- diff - Variable in class etomica.math.numerical.VirialOptimizer
-
- diffDiv(Rgb16, Rgb16, int) - Method in class org.jmol.util.Rgb16
-
- difference(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Generates the set of diagrams obtained by subtracting the second set from the first set.
- diffuseFactor - Static variable in class org.jmol.util.Shader
-
- diffusepercent - Static variable in class org.jmol.script.Token
-
- diffusePercent - Static variable in class org.jmol.util.Shader
-
- DifParameters - Class in etomica.graph.operations
-
- DifParameters(char) - Constructor for class etomica.graph.operations.DifParameters
-
- digits - Variable in class etomica.graphics.DisplayTable
-
- dihedralAngle(Plane) - Method in class etomica.math.geometry.Plane
-
Dihedral angle between this plane and the given plane.
- dim - Variable in class etomica.action.BoxQuench
-
- dim - Variable in class etomica.lattice.IndexIteratorIncreasing
-
- dim - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- dim - Variable in class etomica.modules.adsorption.MyMCMove
-
- dim - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- dim - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- dim - Variable in class etomica.modules.rosmosis.MeterFlux
-
- dim - Variable in class etomica.normalmode.MeterSolidDA
-
- dim - Variable in class etomica.normalmode.MeterSolidDACut
-
- dim - Variable in class etomica.spaceNd.TensorND
-
- dimension - Variable in class etomica.data.DataInfoFactory
-
- dimension() - Method in class etomica.units.CompoundUnit
-
- DIMENSION - Static variable in class etomica.units.dimensions.Angle
-
- DIMENSION - Static variable in class etomica.units.dimensions.Area
-
- DIMENSION - Static variable in class etomica.units.dimensions.Charge
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Current
-
Singleton instance of this class.
- Dimension - Class in etomica.units.dimensions
-
Parent of all Dimension classes, which describe the physical dimensions
(e.g., mass, length, force) of a quantity.
- Dimension(String, double, double, double) - Constructor for class etomica.units.dimensions.Dimension
-
- Dimension(String, double, double, double, double, double, double, double) - Constructor for class etomica.units.dimensions.Dimension
-
- Dimension(String, double[]) - Constructor for class etomica.units.dimensions.Dimension
-
- DIMENSION - Static variable in class etomica.units.dimensions.Dipole
-
- DIMENSION - Static variable in class etomica.units.dimensions.ElectricPotential
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Energy
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Force
-
- DIMENSION - Static variable in class etomica.units.dimensions.Fraction
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Frequency
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Length
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.LuminousIntensity
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Mass
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Momentum
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Null
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Power
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Pressure
-
Singleton instance of this class.
- dimension(int) - Static method in class etomica.units.dimensions.Pressure
-
Returns the Dimension instance for the "pressure" appropriate to the given
dimension.
- DIMENSION - Static variable in class etomica.units.dimensions.Pressure2D
-
- DIMENSION - Static variable in class etomica.units.dimensions.Quantity
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Temperature
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Time
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Undefined
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Velocity
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Viscosity
-
Singleton instance of this class.
- DIMENSION - Static variable in class etomica.units.dimensions.Volume
-
Singleton instance of this class.
- dimension(int) - Static method in class etomica.units.dimensions.Volume
-
Returns the Dimension instance for the "volume" appropriate to the given
dimension.
- DIMENSION - Static variable in class etomica.units.dimensions.Wavenumber
-
Singleton instance of this class.
- dimension() - Method in class etomica.units.PrefixedUnit
-
Returns the dimension of this baseUnit.
- dimension() - Method in class etomica.units.SimpleUnit
-
Returns the dimension of this base unit.
- dimension() - Method in class etomica.units.systems.LJ.LJUnit
-
- dimension() - Method in interface etomica.units.Unit
-
Returns the dimension of the unit.
- Dimensioned - Annotation Type in etomica.units.dimensions
-
- DimensionedDoubleEditor - Class in etomica.graphics
-
Editor to set the value of a double-type property having units associated with it.
- DimensionedDoubleEditor(Dimension) - Constructor for class etomica.graphics.DimensionedDoubleEditor
-
- DimensionRatio - Class in etomica.units.dimensions
-
Class to form a dimension from ratio of two dimensions.
- DimensionRatio(Dimension, Dimension) - Constructor for class etomica.units.dimensions.DimensionRatio
-
- DimensionRatio(String, Dimension, Dimension) - Constructor for class etomica.units.dimensions.DimensionRatio
-
- dimensions() - Method in class etomica.graphics.DisplayPolytope
-
returns dimensions of polytope as the (max - min) value in
each dimension for all the vertices.
- dimensions - Variable in class etomica.space.BoundaryRectangular
-
- dimensions - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
-
- dimensionsHalf - Variable in class etomica.space.BoundaryRectangularPeriodic
-
- dimensionsHalf - Variable in class etomica.space.BoundaryRectangularPore
-
- dimensionsHalf - Variable in class etomica.space.BoundaryRectangularSlit
-
- dimensionsHalf - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
-
- dimensionString() - Static method in class etomica.units.gui.Lister
-
- dimer - Variable in class etomica.dimer.SimDimerMEAMGB
-
- DimerApproach - Class in etomica.models.rowley
-
- DimerApproach() - Constructor for class etomica.models.rowley.DimerApproach
-
- dimerApproach - Variable in class etomica.models.rowley.DimerApproach
-
- dimerAtomType - Variable in class etomica.normalmode.SpeciesHSDimer
-
- dimerColorManager - Variable in class etomica.association.ColorSchemeSmer
-
- dimerCurvature(Vector[], Vector[], Vector[]) - Method in class etomica.dimer.IntegratorDimerRT
-
Computes curvature value, C, for the energy surface.
- dimerForceCenter(Vector[]) - Method in class etomica.dimer.IntegratorDimerRT
-
- dimerForceEff(Vector[], Vector[], Vector[]) - Method in class etomica.dimer.IntegratorDimerRT
-
- dimerForcePerp(Vector[], Vector[], Vector[]) - Method in class etomica.dimer.IntegratorDimerMin
-
Finds the component of the dimer's total force that is perpendicular to the normal vector.
- dimerForcePerp(Vector[], Vector[], Vector[], Vector[]) - Method in class etomica.dimer.IntegratorDimerRT
-
- dimerForces(Vector[], Vector[], Vector[]) - Method in class etomica.dimer.IntegratorDimerMin
-
Resets forces in boxes 0 and min, calls potential.calculate, and copies over
the new forces to local arrays.
- dimerForces(Vector[], Vector[], Vector[]) - Method in class etomica.dimer.IntegratorDimerRT
-
- dimerForcesStar(Vector[], Vector[], Vector[]) - Method in class etomica.dimer.IntegratorDimerMin
-
Used in the middle of the rotateDimer method.
- dimerForcesStar(Vector[], Vector[], Vector[]) - Method in class etomica.dimer.IntegratorDimerRT
-
- dimerNormal() - Method in class etomica.dimer.IntegratorDimerMin
-
Computes an n-dimensional vector in potential energy hyperspace, pointing
in the direction of the dimer (intersecting both simulation boxes).
- dimerNormal() - Method in class etomica.dimer.IntegratorDimerRT
-
- dimerPotential - Variable in class etomica.association.MCMoveDimer
-
- dimerPotential - Variable in class etomica.association.MCMoveDimerRotate
-
- dimerPotential - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- dimerPotential - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- dimerPump - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
-
- dimerSaddleTolerance() - Method in class etomica.dimer.IntegratorDimerRT
-
- dimerUpdatePositions(double, Vector[]) - Method in class etomica.dimer.IntegratorDimerRT
-
- dimVector - Variable in class etomica.action.BoxInflate
-
- dimx - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- dimy - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- dipind(int, int, int[], int[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- dipole - Variable in class etomica.dielectric.TIP4P_NVT.DipoleSourceTIP4PWater
-
- dipole - Variable in class etomica.models.OPLS.DipoleSourceAceticAcid
-
- dipole - Variable in class etomica.models.water.DipoleSourceWater
-
- Dipole - Class in etomica.units.dimensions
-
Base unit for electrical dipole moment.
- dipole() - Method in class etomica.units.systems.CGS
-
- dipole() - Method in class etomica.units.systems.LJ
-
- dipole() - Method in class etomica.units.systems.MKS
-
- dipole() - Method in class etomica.units.systems.UnitSystem
-
- dipole() - Method in class etomica.units.systems.UnitSystem.Sim
-
- dipole - Static variable in class org.jmol.script.Token
-
- DipoleBox - Class in etomica.rotation
-
- DipoleBox(Space, int, double) - Constructor for class etomica.rotation.DipoleBox
-
- DipoleBox.Applet - Class in etomica.rotation
-
- DipoleBoxMatrix - Class in etomica.rotation
-
- DipoleBoxMatrix(Space, int, double) - Constructor for class etomica.rotation.DipoleBoxMatrix
-
- DipoleBoxMatrix.Applet - Class in etomica.rotation
-
- dipoleFShift - Variable in class etomica.rotation.P2LJDipole
-
- dipolescale - Static variable in class org.jmol.script.Token
-
- dipoleSource - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- DipoleSource - Interface in etomica.molecule
-
Interface for something that can calculate the dipole of a molecule.
- dipoleSource - Variable in class etomica.potential.P1ExternalField
-
- dipoleSource - Variable in class etomica.potential.P2ReactionFieldDipole
-
- dipoleSource - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- dipoleSource - Variable in class etomica.potential.PotentialCalculationPhiSum
-
- DipoleSourceAceticAcid - Class in etomica.models.OPLS
-
calculates dipole for acetic acid
- DipoleSourceAceticAcid(Space) - Constructor for class etomica.models.OPLS.DipoleSourceAceticAcid
-
- DipoleSourceDHS(Space, double) - Constructor for class etomica.AlkaneEH.DHS_NVT.DipoleSourceDHS
-
- DipoleSourceDHS(Space, double) - Constructor for class etomica.dielectric.DHS_NVT.DipoleSourceDHS
-
- DipoleSourceDLJ(Space, double) - Constructor for class etomica.AlkaneEH.DLJ_NVT_1site.DipoleSourceDLJ
-
- DipoleSourceDLJ(Space, double) - Constructor for class etomica.dielectric.DLJ_NVT_1site.DipoleSourceDLJ
-
- DipoleSourceTIP4PWater(Space) - Constructor for class etomica.dielectric.TIP4P_NVT.DipoleSourceTIP4PWater
-
- DipoleSourceWater - Class in etomica.models.water
-
Implementation of DipoleSource that can handle water molecules that are
MoleculeOriented.
- DipoleSourceWater(Space) - Constructor for class etomica.models.water.DipoleSourceWater
-
- dipoleStrength - Variable in class etomica.AlkaneEH.DHS_NVT.DipoleSourceDHS
-
- dipoleStrength - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.DipoleSourceDLJ
-
- dipoleStrength - Variable in class etomica.dielectric.DHS_NVT.DipoleSourceDHS
-
- dipoleStrength - Variable in class etomica.dielectric.DLJ_NVT_1site.DipoleSourceDLJ
-
- dipoleStrength - Variable in class etomica.models.water.DipoleSourceWater
-
- dipoleStrength2 - Variable in class etomica.AlkaneEH.DHS_NVT.Param
-
- dipoleStrength2 - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- dipoleStrength2 - Variable in class etomica.dielectric.DHS_NVT.Param
-
- dipoleStrength2 - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- dipoleUShift - Variable in class etomica.rotation.P2LJDipole
-
- dipoleVector - Variable in class etomica.AlkaneEH.DHS_NVT.DipoleSourceDHS
-
- dipoleVector - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.DipoleSourceDLJ
-
- dipoleVector - Variable in class etomica.dielectric.DHS_NVT.DipoleSourceDHS
-
- dipoleVector - Variable in class etomica.dielectric.DLJ_NVT_1site.DipoleSourceDLJ
-
- dir0 - Variable in class etomica.potential.P2SpheroPolyhedron
-
- dir1 - Variable in class etomica.potential.P2SpheroPolyhedron
-
- dir2 - Variable in class etomica.potential.P2SpheroPolyhedron
-
- direction - Variable in class etomica.config.ConfigurationOrientedFile
-
- direction - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- direction - Variable in class etomica.molecule.iterator.MpiIntraspecies1A
-
- direction() - Method in class etomica.potential.IteratorDirective
-
- direction - Variable in class etomica.space2d.Orientation2D
-
- direction - Variable in class etomica.space3d.Orientation3D
-
- direction - Variable in class etomica.space3d.OrientationFull3D
-
- DirectSamplingTargetQCArReferenceAzizAr - Class in etomica.virial.simulations
-
This class used the direct-sampling formulation of Mayer-Sampling Monte Carlo to compute the second
virial coefficient of argon, as described with a quantum potential (via Q-Chem), at a particular temperature.
- DirectSamplingTargetQCArReferenceAzizAr() - Constructor for class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr
-
- DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam - Class in etomica.virial.simulations
-
Inner class for parameters
- dirty - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- dirty - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- dirty - Variable in class etomica.math.numerical.AkimaSpline
-
- disableEnergy() - Method in class etomica.meam.P2EAM
-
- disablepopupmenu - Static variable in class org.jmol.script.Token
-
- DiscardCriteria(char, int, char, int) - Constructor for class etomica.virial.cluster.VirialDiagramsPT.DiscardCriteria
-
- disconnectedP - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- disconnectedP - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- disconnectedP - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- disconnectedP - Variable in class etomica.virial.cluster.VirialDiagrams
-
- disconnectedP - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- disconnectedP - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- disconnectedP - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- disconnectedP - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- disconnectedP - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- disp - Variable in class etomica.potential.P2QChemInterpolated
-
- disp - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
-
- disp - Variable in class etomica.potential.P3QChem.DampingParams
-
- displacementLimit2 - Variable in class etomica.nbr.CriterionSimple
-
- displacementLimit2 - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- display(Parser.CommandVariable) - Method in class etomica.graph.engine.Interpreter
-
- Display - Class in etomica.graphics
-
Superclass of all classes that display something from the simulation.
- Display() - Constructor for class etomica.graphics.Display
-
- display - Variable in class etomica.meam.EFSTungsten
-
- display - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- display - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- display - Variable in class etomica.meam.MEAMMd3D
-
- display - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- display - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- display - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- display - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- display - Variable in class etomica.simulation.prototypes.LJMD2D
-
- display - Variable in class etomica.simulation.prototypes.SWMD2D
-
- display - Variable in class etomica.simulation.prototypes.SWMD3D
-
- display - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- display - Static variable in class org.jmol.script.Token
-
- displayAHarmonic - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- displayAHarmonic - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- displayAHarmonic - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- displayBoundary - Variable in class etomica.graphics.DisplayBox
-
- DisplayBox - Class in etomica.graphics
-
Displays a picture of a box, with configurations of molecules, boundaries, and other objects as appropriate, assuming 2-dimensional system.
- DisplayBox(Simulation, Box) - Constructor for class etomica.graphics.DisplayBox
-
Warning: after instantiation, clients using G3DSys may need to toggle
display.canvas.setVisible false and then true to fix the 'sometimes
gray' bug.
- displayBox - Variable in class etomica.graphics.DisplayCanvas
-
- displayBox - Variable in class etomica.modules.crystalviewer.CrystalViewer
-
- displayBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- DisplayBoxCanvas1D - Class in etomica.graphics
-
- DisplayBoxCanvas1D(Space, DisplayBox, Controller) - Constructor for class etomica.graphics.DisplayBoxCanvas1D
-
- DisplayBoxCanvas1DBins - Class in etomica.modules.entropylottery
-
Class used to define canvas onto which configuration is drawn
- DisplayBoxCanvas1DBins(DisplayBox, Controller) - Constructor for class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
- DisplayBoxCanvas2D - Class in etomica.graphics
-
- DisplayBoxCanvas2D(DisplayBox, Space, Controller) - Constructor for class etomica.graphics.DisplayBoxCanvas2D
-
- DisplayBoxCanvas2DNpTScaling - Class in etomica.normalmode.nptdemo
-
- DisplayBoxCanvas2DNpTScaling(DisplayBox, Space, Controller, CoordinateDefinition) - Constructor for class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- DisplayBoxCanvasG3DSys - Class in etomica.graphics
-
- DisplayBoxCanvasG3DSys(Simulation, DisplayBox, Space, Controller) - Constructor for class etomica.graphics.DisplayBoxCanvasG3DSys
-
- DisplayBoxCanvasG3DSys.OrientedAgentSource - Class in etomica.graphics
-
- DisplayBoxCanvasG3DSys.OrientedFullSite - Class in etomica.graphics
-
- DisplayBoxCanvasG3DSys.OrientedSite - Class in etomica.graphics
-
- displayBoxScaled - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- DisplayBoxSpin2D - Class in etomica.graphics
-
- DisplayBoxSpin2D(DisplayBox, NeighborSiteManager, Space, Controller) - Constructor for class etomica.graphics.DisplayBoxSpin2D
-
- DisplayCanvas - Class in etomica.graphics
-
Superclass for classes that display information from simulation by painting to a canvas.
- DisplayCanvas(Controller) - Constructor for class etomica.graphics.DisplayCanvas
-
Construct a DisplayCanvas using the given controller (which may be null).
- displaycellparameters - Static variable in class org.jmol.script.Token
-
- displayCycles - Variable in class etomica.modules.osmosis.Osmosis
-
- displayCycles - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- displayDensity - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- displayDensity - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- displayed - Variable in class etomica.modules.droplet.EllipseDisplayAction
-
- displayEllipse(double) - Method in class etomica.modules.droplet.EllipseDisplayAction
-
- displayList() - Method in class etomica.graphics.SimulationGraphic
-
- displayList() - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
-
- displayMaxX - Variable in class org.jmol.util.GData
-
- displayMaxY - Variable in class org.jmol.util.GData
-
- displayMinX - Variable in class org.jmol.util.GData
-
- displayMinY - Variable in class org.jmol.util.GData
-
- displayMoleculeList() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- displayMoleculeList() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- displayPanel - Variable in class etomica.modules.clustergenerator.MyApplet
-
- DisplayPlot - Class in etomica.graphics
-
Class for creating a plot of simulation data.
- DisplayPlot() - Constructor for class etomica.graphics.DisplayPlot
-
Creates a plot with a new, empty, DataSinkTable.
- DisplayPlot(DataSet) - Constructor for class etomica.graphics.DisplayPlot
-
Creates a plot using data from the given table.
- displayPlot - Variable in class etomica.graphics.EtomicaPlot
-
- DisplayPlot.DataWriter - Class in etomica.graphics
-
Writes a file with the raw data from a plot.
- DisplayPlot.PopupListener - Class in etomica.graphics
-
- DisplayPlot.RawDataWindowOpener - Class in etomica.graphics
-
Opens a window with the raw data from a plot.
- DisplayPolytope - Class in etomica.graphics
-
Displays a picture of a polytope.
- DisplayPolytope(Polytope) - Constructor for class etomica.graphics.DisplayPolytope
-
- DisplayPolytope.Applet - Class in etomica.graphics
-
- DisplayPolytopeCanvas2D - Class in etomica.graphics
-
- DisplayPolytopeCanvas2D(DisplayPolytope) - Constructor for class etomica.graphics.DisplayPolytopeCanvas2D
-
- DisplayPolytopeCanvasG3DSys - Class in etomica.graphics
-
- DisplayPolytopeCanvasG3DSys(DisplayPolytope) - Constructor for class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
- DisplayScrollingGraph - Class in etomica.graphics
-
- DisplayScrollingGraph() - Constructor for class etomica.graphics.DisplayScrollingGraph
-
- displaySelectedSpecies(int, int) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- DisplayTable - Class in etomica.graphics
-
Presents data in a tabular form.
- DisplayTable() - Constructor for class etomica.graphics.DisplayTable
-
- DisplayTable(DataSinkTable) - Constructor for class etomica.graphics.DisplayTable
-
- displayTable - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- displayTable - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- displayTableEigen - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- displayTableWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- DisplayTextBox - Class in etomica.graphics
-
A simple display of a single value in a textbox with an associated label.
- DisplayTextBox() - Constructor for class etomica.graphics.DisplayTextBox
-
- DisplayTextBox.LabelType - Enum in etomica.graphics
-
Typed constant used to indicate the type of label to be used with the display.
- DisplayTextBoxesCAE - Class in etomica.graphics
-
Display that presents three boxes with the current value, average,
and error, respectively, given by an AccumulatorAverage.
- DisplayTextBoxesCAE() - Constructor for class etomica.graphics.DisplayTextBoxesCAE
-
- DisplayTimer - Class in etomica.graphics
-
DisplayBox to present the elapsed time in a
molecular dynamics simulation.
- DisplayTimer(IntegratorMD) - Constructor for class etomica.graphics.DisplayTimer
-
- dispose() - Method in class etomica.atom.AtomLeafAgentManager
-
Notifies the AtomAgentManager it should disconnect itself as a listener and release all of its agents.
- dispose() - Method in class etomica.atom.AtomTypeAgentManager
-
Unregisters this class as a listener for AtomType-related events and releases its agents.
- dispose() - Method in class etomica.box.BoxAgentManager
-
Notifies the BoxAgentManager that it should release all agents and
stop listening for events from the simulation.
- dispose() - Method in class etomica.graphics.DisplayCanvas
-
- dispose() - Method in class etomica.graphics.DisplayTimer
-
Unhooks the DisplayTimer from the integrator
- dispose() - Method in class etomica.molecule.MoleculeAgentManager
-
Notifies the AtomAgentManager it should disconnect itself as a listener.
- dispose() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- dispose() - Method in class etomica.nbr.list.NeighborListManager
-
- dispose() - Method in class etomica.species.SpeciesAgentManager
-
Unregisters this class as a listener for AtomType-related events and
releases its agents.
- dispose() - Method in class etomica.util.random.RandomNumberGeneratorUnix
-
Cleanup, close the file.
- disposeGraphics(Object) - Method in interface org.jmol.api.ApiPlatform
-
- disposeGraphics(Object) - Method in class org.jmol.awt.Platform
-
- disproportionate(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
this function will makes a and b unreactive by setting both to be bonded
to themselves (a-a, b-b).
- distance - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- distance - Variable in class etomica.virial.ConfigurationClusterMove
-
- distance - Static variable in class org.jmol.script.Token
-
- distance(Point3f) - Method in class org.jmol.util.Point3f
-
Returns the distance between this point and point p1.
- distance(Point4f) - Method in class org.jmol.util.Point4f
-
Returns the distance between this point and point p1.
- distanceSquared(Point3f) - Method in class org.jmol.util.Point3f
-
Computes the square of the distance between this point and point p1.
- distanceTo(Vector) - Method in class etomica.math.geometry.Plane
-
Perpendicular distance from the plane to the given point.
- distanceTo(Vector) - Method in class etomica.math.geometry.Polyhedron
-
Returns the perpendicular distance to the nearest face of the
polyhedron.
- distanceTo(Vector) - Method in class etomica.modules.pistoncylinder.PistonPlane
-
- distanceTo(Vector) - Method in class etomica.modules.sam.WallPlane
-
- distanceToPlane(Point4f, Point3f) - Static method in class org.jmol.util.Measure
-
- distanceToPlane(Vector3f, float, Point3f) - Static method in class org.jmol.util.Measure
-
- distanceToPlaneD(Point4f, float, Point3f) - Static method in class org.jmol.util.Measure
-
- distPol - Variable in class etomica.models.water.P2WaterSzalewicz
-
- Distribution(Space, double, double) - Constructor for class etomica.statmech.MaxwellBoltzmann.Distribution
-
- div(Complex) - Method in class etomica.math.Complex
-
Division of Complex numbers (doesn't change this Complex number).
- div(Quaternion) - Method in class org.jmol.util.Quaternion
-
- div(Quaternion[], Quaternion[], int, boolean) - Static method in class org.jmol.util.Quaternion
-
- divide(Coefficient) - Method in interface etomica.graph.model.Coefficient
-
- divide(Coefficient) - Method in class etomica.graph.model.impl.CoefficientImpl
-
- divide(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurd
-
Divide by another square root.
- divide(BigInteger) - Method in class etomica.veos.bigdecimal.BigSurd
-
Divide by an integer.
- divide(int) - Method in class etomica.veos.bigdecimal.BigSurd
-
Divide by an integer.
- divide(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor
-
Integer division through another positive integer.
- divide(Rational) - Method in class etomica.veos.bigdecimal.Rational
-
Divide by another fraction.
- divide(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
Divide by an integer.
- divide(int) - Method in class etomica.veos.bigdecimal.Rational
-
Divide by an integer.
- divideAndRemainder(BigIntegerPoly) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Divide by another polynomial.
- divideRound(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Divide and round.
- divideRound(BigComplex, BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Divide and round.
- divideRound(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Divide and round.
- divideRound(BigDecimal, BigInteger) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Divide and round.
- divideRound(BigInteger, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Divide and round.
- divideRound(BigInteger, BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Divide and round.
- divideRound(int, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Divide and round.
- divisor - Variable in class etomica.potential.Potential0Lrc
-
- divisors(BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Compute the list of positive divisors.
- divisors() - Method in class etomica.veos.bigdecimal.Ifactor
-
The set of positive divisors.
- divLeft(Quaternion) - Method in class org.jmol.util.Quaternion
-
- DLGA(double) - Static method in class etomica.math.Gamma
-
- DLJ_NVT_1site - Class in etomica.AlkaneEH
-
Canonical ensemble Monte Carlo simulation (NVT)
calculate dielectric constant epsilon for dipolar LJ model
- DLJ_NVT_1site(Space, int, double, double, double, double, double, double, double) - Constructor for class etomica.AlkaneEH.DLJ_NVT_1site
-
- DLJ_NVT_1site - Class in etomica.dielectric
-
Canonical ensemble Monte Carlo simulation (NVT)
calculate dielectric constant epsilon for dipolar LJ model
- DLJ_NVT_1site(Space, int, double, double, double, double, double, double, double) - Constructor for class etomica.dielectric.DLJ_NVT_1site
-
- DLJ_NVT_1site.DipoleSourceDLJ - Class in etomica.AlkaneEH
-
- DLJ_NVT_1site.DipoleSourceDLJ - Class in etomica.dielectric
-
- DLJ_NVT_1site.Param - Class in etomica.AlkaneEH
-
- DLJ_NVT_1site.Param - Class in etomica.dielectric
-
- dmptab - Variable in class etomica.models.water.P2WaterSzalewicz
-
- dn - Variable in class etomica.potential.P3HydrogenManzhos
-
- dna - Static variable in class org.jmol.script.Token
-
- do21 - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
-
- doAction(IAction) - Method in class etomica.graphics.Device
-
Method called by subclasses to execute the action of the device.
- doAction(IAction) - Method in class etomica.graphics.DeviceSlider
-
- doActionNow(IAction) - Method in class etomica.action.activity.Controller
-
Pauses current activity, executes given action, then resumes current
activity.
- doAdjustStepFrac - Variable in class etomica.overlap.IntegratorOverlap
-
- doAdjustStepsOnTime - Variable in class etomica.overlap.IntegratorOverlap
-
- doAggressiveAdjustStepFrac - Variable in class etomica.overlap.IntegratorOverlap
-
- doApplyPBC - Variable in class etomica.action.WriteConfiguration
-
- doApplyPBC - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- doApplyPBC - Variable in class etomica.nbr.cell.NeighborCellManager
-
- doApplyPBC - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- doApplyPBC - Variable in class etomica.nbr.list.NeighborListManager
-
- doAveraging - Variable in class etomica.data.histogram.HistogramNotSoSimple
-
- doAvgDef - Variable in class etomica.normalmode.DataSourceFE
-
- doBlockSum() - Method in class etomica.data.AccumulatorAverageCollapsing
-
Performs the block sum after blockSize calls to addData.
- doBlockSum() - Method in class etomica.data.AccumulatorAverageCovariance
-
- doBlockSum() - Method in class etomica.data.AccumulatorAverageFixed
-
Performs the block sum after blockSize calls to addData.
- doBlockSum() - Method in class etomica.data.AccumulatorAverageFixedOutputFile
-
Performs the block sum after blockSize calls to addData.
- doBlockSum() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- doCaching - Variable in class etomica.virial.ClusterSum
-
- doCaching - Variable in class etomica.virial.ClusterSumPolarizable
-
- doCaching - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- doCaching - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- doCaching - Variable in class etomica.virial.ClusterWheatleySoft
-
- doCaching - Variable in class etomica.virial.ClusterWheatleySoftBD
-
- doCaching - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- doCaching - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.data.meter.PotentialCalculationRDF
-
- doCalculation(IAtomList, IPotential) - Method in class etomica.dimer.PotentialCalculationForcePressureSumGB
-
Adds forces due to given potential acting on the atoms produced by the iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.freeenergy.npath.PotentialCalculationDUDW
-
- doCalculation(IAtomList, IPotential) - Method in class etomica.integrator.IntegratorGear4NPH.ForceSumNPH
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
-
Adds forces due to given potential acting on the atoms produced by the iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.liquidLJ.PotentialCalculationSumCutoffLS
-
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.meam.PotentialCalculationEnergySumEAM
-
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.materialfracture.PotentialCalculationForceStress
-
Adds forces due to given potential acting on the atoms produced by the iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
-
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
- doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationEFSSP
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationLJSP
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
Adds forces due to given potential acting on the atoms produced by the iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
Adds forces due to given potential acting on the atoms produced by the iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCutLS
-
Adds forces due to given potential acting on the atoms produced by the iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in interface etomica.potential.PotentialCalculation
-
Method giving the specific calculation performed by this class.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationEnergySum
-
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms.
- doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationEnergySum
-
Adds to the energy sum the energy values obtained from application of the given potential to the
molecules.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
- doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
Adds to the energy sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationForcePressureSum
-
Adds forces due to given potential acting on the atoms produced by the iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationForceSum
-
Adds forces due to given potential acting on the atoms produced by the iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationHyperVirialSum
-
Adds to the virial sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
- doCalculation(IMoleculeList, IPotentialMolecular) - Method in interface etomica.potential.PotentialCalculationMolecular
-
Method giving the specific calculation performed by this class.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationMolecularVirialSum
-
- doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationMolecularVirialSum
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationPhiSum
-
- doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationPhiSum
-
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationPressureTensor
-
Adds the pressure tensor contribution based on the forces acting on each
pair of atoms produced by the iterator.
- doCalculation(IMoleculeList, IPotentialMolecular) - Method in class etomica.potential.PotentialCalculationTorqueSum
-
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationTorqueSum
-
Adds forces and torques due to given potential acting on the atoms produced by the iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.potential.PotentialCalculationVirialSum
-
Adds to the virial sum the energy values obtained from application of the given potential to the
atoms produced by the given iterator.
- doCalculation(IAtomList, IPotentialAtomic) - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- doChainRef - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
-
- doChainRef - Variable in class etomica.virial.simulations.VirialLJD.VirialLJParam
-
- doClear - Variable in class etomica.graphics.DisplayPlot
-
- doCommand(String, StatusAction) - Method in class etomica.server.resources.ControlResource
-
- doConfigButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- doContinue() - Method in class etomica.action.Activity
-
- doCopy - Variable in class etomica.graph.iterators.IteratorWrapper
-
- doCorrection - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- doCorti - Variable in class etomica.normalmode.MCMoveVolumeSolid
-
- doCov - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- doCov - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- doCov - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- doD2 - Variable in class etomica.normalmode.MeterSolidDA
-
- doD2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- dodebug - Static variable in class etomica.association.MCMoveAtomSmer
-
- dodebug - Static variable in class etomica.association.MCMoveMoleculeSmer
-
- dodebug - Static variable in class etomica.association.MCMoveVolumeAssociated
-
- dodebug - Static variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- dodebug - Static variable in class etomica.integrator.IntegratorMC
-
- doDensityInput - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- doDiff - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- doDisconnectedMatching - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doDisconnectedMatching - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- doDisconnectedMatching - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doDouble - Variable in class etomica.modules.rheology.MeterNormalStress
-
- doDown - Variable in class etomica.lattice.RectangularLatticeNbrIterator
-
- doEigenDecompose(double[][], String) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- doEigenDecompose(double[][], String) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- doEigenDecomposeAndFile(double[][], String) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- doEnforceBounds - Variable in class etomica.data.DataSourceUniform
-
- doExchange - Variable in class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
-
- doExchange - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doExchange - Variable in class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
-
- doExchange - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doExchangeCondensing - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doExchangeCondensing - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doExchangeF - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doExchangeF - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doExcludeNonNeighbors - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- doExcludeNonNeighbors - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- doExcludeNonNeighbors - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- doExp - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doExp - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
-
- doExpDensityprofile - Variable in class etomica.virial.cluster.ExternalVirialDiagrams
-
- doFancyMonoclinic - Static variable in class etomica.normalmode.HSDimerNPT
-
- doFancyOriented - Static variable in class etomica.normalmode.HSDimerNPT
-
- doFastButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- doFindMinimum(double[], double[], double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- doFindMinimum(double[], double[], double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- doFindMinimum(double[], double[], double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- doFindMinimum(double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- doFit(double[], double[]) - Static method in class etomica.math.numerical.LinearFit
-
- doFit(double[], double[], double[]) - Static method in class etomica.math.numerical.LinearFit
-
- doFit(int, double[], double[]) - Static method in class etomica.math.numerical.PolynomialFit
-
Perform polynomial fit of the given order.
- doFit(int, double[], double[], double[]) - Static method in class etomica.math.numerical.PolynomialFit
-
Perform polynomial fit of the given order with the given weights (w).
- doFit(double[], double[]) - Method in class etomica.modules.interfacial.FitTanh
-
- doFit(double[], double[]) - Method in class etomica.surfacetension.FitTanh
-
- doFlip(IMolecule) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- doFlip(IMolecule) - Method in class etomica.association.BiasVolumeAceticAcid
-
- doGlobalMoves() - Method in class etomica.integrator.IntegratorManagerMC
-
Method to select and perform an elementary Monte Carlo move.
- doGoDown - Variable in class etomica.atom.iterator.TripletInnerSequential
-
- doGoDown - Variable in class etomica.molecule.iterator.MpiIntraspecies1A
-
- doGoUp - Variable in class etomica.atom.iterator.TripletInnerSequential
-
- doGradientNoShift(Vector, Vector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- doGradientShift(Vector, Vector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- doGraphics - Static variable in class etomica.normalmode.HSDimerNPT
-
- doHarmonic - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- doHB - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doHB - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doHist - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
-
- doHist - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
-
- doHist - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
-
- doHist - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- doHist - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
-
- doHist - Variable in class etomica.virial.simulations.VirialH2OGCPMD.VirialParam
-
- doHist - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- doHist - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- doHist - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- doHist - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- doHist - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- doHist - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- doHist - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
-
- doHist - Variable in class etomica.virial.simulations.VirialLJD.VirialLJParam
-
- doHist - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- doHist - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- doHistory - Variable in class etomica.meam.EFSTungsten.Params
-
- doIgnoreRefAvg - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- doIncludeACInError - Variable in class etomica.data.AccumulatorAverage
-
- doIncludeACInError() - Method in class etomica.data.AccumulatorAverage
-
- doIncludePair - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- doIncludePair - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- doInterpolateHole() - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- doInterpolateHole2() - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- doInterpolation(double[]) - Method in class etomica.math.numerical.AkimaSpline
-
- doInterpolationDy(double[]) - Method in class etomica.math.numerical.AkimaSpline
-
- doit(NormalModes, int, double, int) - Static method in class etomica.normalmode.CalcHarmonicA
-
- doit(String, int) - Static method in class etomica.normalmode.NormalModeEigenGetter
-
- doit(String) - Static method in class etomica.paracetamol.NormalModeEigenGetter
-
- doJustTilt - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp.PlotAction
-
- doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- doKeepEBonds - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doLatticeSum - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- doLatticeSum - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- doLatticeSum - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- doLogLevel(boolean) - Static method in class org.jmol.util.Logger
-
Indicates if the level is logged.
- doMinimalBC - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doMinimalBC - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- doMinimalBC - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doMinimalMulti - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doMinimalMulti - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- doMinimalMulti - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doMulti - Variable in class etomica.virial.ClusterWheatleyMultibody
-
- doMulti - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
-
- doMulti - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- doMulti - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- doMulti - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
-
- doMultiFromPair - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doMultiFromPair - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doNBodyStuff(IMolecule, PotentialCalculation, int, IPotentialMolecular, NeighborListManagerMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Invokes the PotentialCalculationMolecular for the given Molecule with its up and down
neighbors as a single MoleculeSet.
- doNBodyStuff(IAtom, PotentialCalculation, int, IPotentialAtomic, NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList
-
Invokes the PotentialCalculation for the given Atom with its up and down
neighbors as a single AtomSet.
- doNBodyStuff(IAtom, PotentialCalculation, int, IPotentialAtomic) - Method in class etomica.threaded.atom.PotentialMasterListWorker
-
- doNBodyStuff(IAtom, PotentialCalculation, int, IPotentialAtomic) - Method in class etomica.threaded.domain.PotentialMasterListWorker
-
- done - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- doNegativeExchange - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doNegativeExchange - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doNMoleculeSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- doNonEquilibrium - Variable in class etomica.potential.PotentialCalculationPressureTensor
-
- DooDad(int) - Constructor for class etomica.virial.simulations.VirialHSBinMultiThreaded.DooDad
-
- doOverwrite - Variable in class etomica.normalmode.WriteS
-
- doPaint(Graphics) - Method in class etomica.graphics.DisplayBoxCanvas1D
-
doPaint is the method that handles the drawing of the box to the screen.
- doPaint(Graphics) - Method in class etomica.graphics.DisplayBoxCanvas2D
-
Method that handles the drawing of the box to the screen.
- doPaint(Graphics) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- doPaint(Graphics) - Method in class etomica.graphics.DisplayCanvas
-
- doPaint(Graphics) - Method in class etomica.graphics.DisplayPolytopeCanvas2D
-
doPaint is the method that handles the drawing of the box to the screen.
- doPaint(Graphics) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
- doPaint(Graphics) - Method in class etomica.graphics.DisplayScrollingGraph
-
- doPaint(Graphics) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
doPaint is the method that handles the drawing of the box to the screen.
- doParse(String, Space) - Static method in class etomica.virial.simulations.ShapeParser
-
- doParseArgs(ParameterBase, String[]) - Static method in class etomica.util.ParseArgs
-
- doPBC - Variable in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
-
- doPBC - Variable in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
-
- doPrevious - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- doq2 - Variable in class etomica.freeenergy.npath.SimLattice.LjMC3DParams
-
- doRandStep() - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- doRDF - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- doRealSum - Variable in class etomica.potential.EwaldSummation
-
- doReeHoover - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- doReeHoover - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- doReeHoover - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- doReeHoover - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doReeHoover - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- doReeHoover - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- doReeHoover - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doReeHoover - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- doReeHoover - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- dorefpref - Variable in class etomica.virial.simulations.VirialH2OGCPMD.VirialParam
-
- doResetFilter - Variable in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- doResize - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- doReweight - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
-
- doReweight - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- doReweight - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- doReweight - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- doRing - Variable in class etomica.virial.ClusterChainSoft
-
- doRot - Static variable in class etomica.normalmode.HSDimerNPT
-
- doRotation(int, IMolecule, double, double) - Method in class etomica.models.water.P2Water4PSoft
-
- doRotationTransform(double, double) - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- doScaling - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- doScaling - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- doScaling - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- doSearch(int, int) - Method in class etomica.virial.ClusterSumMultibody
-
- doSecDerXrNoShift(Vector, Vector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- doSecDerXrRotRotNoShift(Vector, Vector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- doSecDerXrRotRotWShift(Vector, Vector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- doSecDerXrWShift(Vector, Vector, double) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- doSerialize - Variable in class etomica.meta.wrappers.Wrapper
-
- doSerialize() - Method in class etomica.meta.wrappers.Wrapper
-
- doSfac - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam
-
- doShape - Static variable in class etomica.normalmode.HSDimerNPT
-
- doShiftInitY() - Method in class etomica.math.numerical.AkimaSplineSmootherDy
-
- doShortcut - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- doShortcut - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- doShortcut - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- doShortcut - Variable in class etomica.virial.cluster.VirialDiagrams
-
- doShortcut - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- doShortcut - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- doShortcut - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- doShortcut - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- doShortcut - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- doShowCurrent - Variable in class etomica.graphics.DisplayTextBoxesCAE
-
- doStatistics - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- doStep() - Method in class etomica.integrator.Integrator
-
Performs the elementary integration step, such as a molecular dynamics
time step, or a Monte Carlo trial.
- doStep() - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- doStep() - Method in class etomica.math.numerical.AkimaSplineSmootherDy
-
- doStepInternal() - Method in class etomica.action.IntegratorDimerApproach
-
- doStepInternal() - Method in class etomica.dimer.IntegratorDimerMin
-
- doStepInternal() - Method in class etomica.dimer.IntegratorDimerRT
-
- doStepInternal() - Method in class etomica.dimer.IntegratorEnergyMap
-
- doStepInternal() - Method in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- doStepInternal() - Method in class etomica.freeenergy.npath.IntegratorImageMultistepMD
-
- doStepInternal() - Method in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- doStepInternal() - Method in class etomica.integrator.Integrator
-
Performs the elementary integration step, such as a molecular dynamics
time step, or a Monte Carlo trial.
- doStepInternal() - Method in class etomica.integrator.IntegratorAnalytic
-
- doStepInternal() - Method in class etomica.integrator.IntegratorConNVT
-
- doStepInternal() - Method in class etomica.integrator.IntegratorGear4
-
- doStepInternal() - Method in class etomica.integrator.IntegratorGear4NPH
-
- doStepInternal() - Method in class etomica.integrator.IntegratorHard
-
Steps all atoms across time interval timeStep, handling all intervening collisions.
- doStepInternal() - Method in class etomica.integrator.IntegratorManagerMC
-
Performs a Monte Carlo trial that attempts to swap the configurations
between two "adjacent" boxes, or instructs all integrators to perform
a single doStep.
- doStepInternal() - Method in class etomica.integrator.IntegratorMC
-
Method to select and perform an elementary Monte Carlo move and decide acceptance.
- doStepInternal() - Method in class etomica.integrator.IntegratorMD
-
- doStepInternal() - Method in class etomica.integrator.IntegratorRigidIterative
-
- doStepInternal() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- doStepInternal() - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- doStepInternal() - Method in class etomica.integrator.IntegratorVelocityVerletRattle
-
- doStepInternal() - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- doStepInternal() - Method in class etomica.integrator.IntegratorVerlet
-
- doStepInternal() - Method in class etomica.kmc.IntegratorKMC
-
- doStepInternal() - Method in class etomica.kmc.IntegratorKMCCluster
-
- doStepInternal() - Method in class etomica.math.numerical.AkimaSplineSmootherApp.IntegratorSmoother
-
- doStepInternal() - Method in class etomica.math.numerical.AkimaSplineSmootherDyApp.IntegratorSmoother
-
- doStepInternal() - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- doStepInternal() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- doStepInternal() - Method in class etomica.modules.droplet.IntegratorDroplet
-
- doStepInternal() - Method in class etomica.modules.joulethomson.IntegratorJT
-
- doStepInternal() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
-
- doStepInternal() - Method in class etomica.modules.rheology.IntegratorPolymer
-
- doStepInternal() - Method in class etomica.modules.sam.IntegratorVelocityVerletSAM
-
- doStepInternal() - Method in class etomica.normalmode.IntegratorHarmonic
-
- doStepInternal() - Method in class etomica.overlap.IntegratorOverlap
-
- doStepInternal() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- doStepInternal() - Method in class etomica.thermointegration.IntegratorThermodynamic
-
Performs a step in the subIntegrator.
- doStepInternal() - Method in class etomica.tmmc.IntegratorTMMC
-
Method to select and perform an elementary Monte Carlo move.
- doStepInternal() - Method in class etomica.virial.overlap.IntegratorOverlap
-
- doStrictBlockData - Variable in class etomica.data.AccumulatorAverageFixed
-
- doSubtractComb - Variable in class etomica.normalmode.DataSourceFE
-
- doSum112(double[], double[], double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- doSum113(double[], double[], double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- doSum122(double[], double[], double[], double[], double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- doSum644(double[], double[], double[], double[], double, double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- doSum660(double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- doSum734(double[], double[], double[], double[], double, double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- doSum770(double[], double[], double[]) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- doSum833(double[], double[], double[], double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- doSum860(double[], double[], double) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- doSums(double[], double) - Method in class etomica.data.AccumulatorAverageBootstrap
-
Performs the block sum after
- doSums(double[], double) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Performs the block sum after
- doSurfacetension - Variable in class etomica.virial.cluster.ExternalVirialDiagrams
-
- doSwap - Variable in class etomica.atom.iterator.ApiInnerVariable
-
- doSwap - Variable in class etomica.molecule.iterator.MpiInnerVariable
-
- dot(Vector) - Method in interface etomica.space.Vector
-
Returns the dot product of this vector with the given one.
- dot(Vector) - Method in class etomica.space1d.Vector1D
-
- dot(Vector) - Method in class etomica.space2d.Vector2D
-
- dot(Vector) - Method in class etomica.space3d.Vector3D
-
- dot(Vector) - Method in class etomica.spaceNd.VectorND
-
- dot(Quaternion) - Method in class org.jmol.util.Quaternion
-
- dot(Vector3f) - Method in class org.jmol.util.Vector3f
-
Computes the dot product of the this vector and vector v.
- dotdensity - Static variable in class org.jmol.script.Token
-
- doThermostat() - Method in class etomica.integrator.IntegratorMD
-
Invokes thermostat, modifying velocities according to specified temperature and
algorithm of thermostat specified via setThermostat.
- doThermostat() - Method in class etomica.normalmode.IntegratorHardMDMC
-
- doThermostat() - Method in class etomica.normalmode.IntegratorHarmonic
-
- doThermostatInternal() - Method in class etomica.integrator.IntegratorMD
-
Fires the thermostat if the appropriate interval has been reached.
- doThermostatInternal() - Method in class etomica.modules.rheology.IntegratorPolymer
-
- doTotal - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- doTotal - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- doTotal - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- doTotal - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- doTotal - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- doTotal - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- doTotal - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- doTransform(IMolecule, Vector, Vector, double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- doTransform(IMolecule, Vector, Vector, double) - Method in class etomica.association.BiasVolumeAceticAcid
-
- doTransform(IMolecule, Vector) - Method in class etomica.association.MCMoveBiasUBMolecule
-
- doTransform(IAtom) - Method in class etomica.association.MCMoveDimerRotate
-
- doTransform(IAtomOriented) - Method in class etomica.association.MCMoveSmerRotate
-
- doTransform(IAtom) - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- doTransform() - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- doTransform(IMolecule, Boundary, Tensor) - Static method in class etomica.models.clathrates.MinimizationTIP4P
-
- doTransform() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- doTransform() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- doTransform(IMolecule, Vector) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- doTransform(IMolecule, IMoleculePositionDefinition, Tensor) - Static method in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- doTransform(IMolecule, IMoleculePositionDefinition, Tensor) - Static method in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- doTransform(IMolecule, Vector, RotationTensor) - Static method in class etomica.models.water.OrientationCalcWater3P
-
- doTransform(IMolecule, Vector, RotationTensor) - Static method in class etomica.models.water.OrientationCalcWater4P
-
- doTransform(IMolecule) - Method in class etomica.models.water.P2Water4PSoft
-
- doTransform() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- doTransform(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- doTransform(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- doTransformMolec(int, double) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- doTransformPhi(IMolecule) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- doTransformTheta(IMolecule, double, double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- doTransformToInitial(int, double) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- doTrial() - Method in class etomica.association.MCMoveAtomSmer
-
- doTrial() - Method in class etomica.association.MCMoveBiasUB
-
- doTrial() - Method in class etomica.association.MCMoveBiasUBMolecule
-
- doTrial() - Method in class etomica.association.MCMoveDimer
-
Method to perform trial move.
- doTrial() - Method in class etomica.association.MCMoveDimerRotate
-
Method to perform trial move.
- doTrial() - Method in class etomica.association.MCMoveMoleculeRotateAssociated
-
- doTrial() - Method in class etomica.association.MCMoveMoleculeSmer
-
- doTrial() - Method in class etomica.association.MCMoveRotateAssociated
-
- doTrial() - Method in class etomica.association.MCMoveSmer
-
Method to perform trial move.
- doTrial() - Method in class etomica.association.MCMoveSmerRotate
-
Method to perform trial move.
- doTrial() - Method in class etomica.association.MCMoveVolumeAssociated
-
- doTrial() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- doTrial() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
Method to perform trial move.
- doTrial() - Method in class etomica.freeenergy.npath.MCMoveAtomNPath
-
Method to perform trial move.
- doTrial() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
Method to perform trial move.
- doTrial() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMove
-
Method to perform trial move.
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveAtom
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveAtomInRegion
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveDimer
-
Method to perform trial move.
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
Method to perform trial move.
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
Chooses and performs with equal probability an elementary molecule insertion
or deletion.
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveRotate
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
-
- doTrial() - Method in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- doTrial() - Method in class etomica.interfacial.MCMoveAtomNbr
-
- doTrial() - Method in class etomica.models.hexane.MCMoveCBMC
-
- doTrial(IMolecule) - Method in class etomica.models.hexane.MCMoveCBMC
-
- doTrial() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- doTrial() - Method in class etomica.models.hexane.MCMoveReptate
-
method to perform a trial move.
- doTrial() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- doTrial() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- doTrial() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- doTrial() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- doTrial() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- doTrial() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- doTrial() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- doTrial() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- doTrial() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- doTrial() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- doTrial() - Method in class etomica.modules.adsorption.MyMCMove
-
Chooses and performs with equal probability an elementary molecule insertion
or deletion.
- doTrial() - Method in class etomica.modules.dcvgcmd.MyMCMove
-
Chooses and performs with equal probability an elementary molecule insertion
or deletion.
- doTrial() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
Method to perform trial move.
- doTrial() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- doTrial() - Method in class etomica.modules.vle.MCMoveMoleculeExchangeVLE
-
- doTrial() - Method in class etomica.modules.vle.MCMoveVolumeExchangeVLE
-
- doTrial() - Method in class etomica.normalmode.MCMoveAtomCoupled
-
Method to perform trial move.
- doTrial() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
Method to perform trial move.
- doTrial() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
Method to perform trial move.
- doTrial() - Method in class etomica.normalmode.MCMoveAtomSuperBox
-
Method to perform trial move.
- doTrial() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- doTrial() - Method in class etomica.normalmode.MCMoveHarmonic
-
- doTrial() - Method in class etomica.normalmode.MCMoveHarmonicEin
-
- doTrial() - Method in class etomica.normalmode.MCMoveHarmonicStep
-
- doTrial() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
- doTrial() - Method in class etomica.normalmode.MCMovePhaseAngle
-
- doTrial() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- doTrial() - Method in class etomica.normalmode.MCMoveSingleMode
-
- doTrial() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- doTrial() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- doTrial() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- doTrial() - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- doTrial() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- doTrial() - Method in class etomica.normalmode.MCMoveWV
-
- doTrial() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- doTrial() - Method in class etomica.spin.MCMoveSpinFlip
-
- doTrial() - Method in class etomica.virial.MCMoveChangeBondLength
-
- doTrial() - Method in class etomica.virial.MCMoveClusterAngleBend
-
- doTrial() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- doTrial() - Method in class etomica.virial.MCMoveClusterAtom
-
- doTrial() - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
-
- doTrial() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
-
- doTrial() - Method in class etomica.virial.MCMoveClusterAtomHSChain
-
- doTrial() - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
- doTrial() - Method in class etomica.virial.MCMoveClusterAtomHSTree
-
- doTrial() - Method in class etomica.virial.MCMoveClusterAtomMulti
-
- doTrial() - Method in class etomica.virial.MCMoveClusterAtomQ
-
- doTrial() - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
-
- doTrial() - Method in class etomica.virial.MCMoveClusterDiagram
-
- doTrial() - Method in class etomica.virial.MCMoveClusterMolecule
-
- doTrial() - Method in class etomica.virial.MCMoveClusterMoleculeLayerMove
-
- doTrial() - Method in class etomica.virial.MCMoveClusterMoleculeMulti
-
- doTrial() - Method in class etomica.virial.MCMoveClusterPolyhedraChain
-
- doTrial() - Method in class etomica.virial.MCMoveClusterPolyhedraTree
-
- doTrial() - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- doTrial() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- doTrial() - Method in class etomica.virial.MCMoveClusterRingRegrow
-
- doTrial() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- doTrial() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- doTrial() - Method in class etomica.virial.MCMoveClusterRingScale
-
- doTrial() - Method in class etomica.virial.MCMoveClusterRotateCH3
-
- doTrial() - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- doTrial() - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- doTrial() - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- doTrial() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- doTrial() - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- doTrial() - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- doTrial() - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- doTrial() - Method in class etomica.virial.MCMoveClusterWiggleMulti
-
- doTrial() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
-
- dots - Static variable in class org.jmol.script.Token
-
- dotscale - Static variable in class org.jmol.script.Token
-
- dotsselectedonly - Static variable in class org.jmol.script.Token
-
- dotsurface - Static variable in class org.jmol.script.Token
-
- DoubleAssociationSitesFluid2Pt - Class in etomica.virial.simulations
-
- DoubleAssociationSitesFluid2Pt() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt
-
- DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- DoubleAssociationSitesFluid3Pt - Class in etomica.virial.simulations
-
- DoubleAssociationSitesFluid3Pt() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt
-
- DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- DoubleAssociationSitesFluid4Pt - Class in etomica.virial.simulations
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's double attraction-site model, hyper-point diagram
4 point diagram calculation
- DoubleAssociationSitesFluid4Pt() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt
-
- DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- DoubleIntegral - Class in etomica.models.oneDHardRods
-
- DoubleIntegral(double, double, double, double, int, int) - Constructor for class etomica.models.oneDHardRods.DoubleIntegral
-
- DoubleIntegralEtas - Class in etomica.models.oneDHardRods
-
Please note this class is specifically designed to integrate for 2 or 3
rod systems, with one rod per cell.
- DoubleIntegralEtas(int, double, double) - Constructor for class etomica.models.oneDHardRods.DoubleIntegralEtas
-
- doubleLength(Object) - Static method in class org.jmol.util.ArrayUtil
-
Very important that this not be used with Int32Array or Float32Array,
because it is not initialized to all zeros in MSIE 9.
- doubleLengthBool(boolean[]) - Static method in class org.jmol.util.ArrayUtil
-
- doubleLengthByte(byte[]) - Static method in class org.jmol.util.ArrayUtil
-
- doubleLengthF(float[]) - Static method in class org.jmol.util.ArrayUtil
-
- doubleLengthI(int[]) - Static method in class org.jmol.util.ArrayUtil
-
- doubleLengthS(String[]) - Static method in class org.jmol.util.ArrayUtil
-
- doubleLengthShort(short[]) - Static method in class org.jmol.util.ArrayUtil
-
- DoubleRange - Class in etomica.math
-
- DoubleRange(double, double) - Constructor for class etomica.math.DoubleRange
-
Constructs the range defined by given values.
- doubleValue() - Method in class etomica.veos.bigdecimal.BigSurd
-
Return a double value representation.
- doubleValue() - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Construct an approximate floating point representation
- doubleValue() - Method in class etomica.veos.bigdecimal.Rational
-
Return a double value representation.
- DoubleWrapper() - Constructor for class etomica.nbr.CriterionPositionWall.DoubleWrapper
-
- doUntransform - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- doUp - Variable in class etomica.lattice.RectangularLatticeNbrIterator
-
- doUpdate() - Method in class etomica.graphics.DeviceBox
-
Updates the display of the box with the current value given by the modifier.
- doUpdate() - Method in class etomica.graphics.DeviceSlider
-
- doUpdate() - Method in class etomica.graphics.DeviceSpinner
-
- doUpdate() - Method in class etomica.graphics.DisplayPlot
-
Redraws the plot.
- doUpdate() - Method in class etomica.graphics.DisplayPolytope
-
- doUpdate() - Method in class etomica.graphics.DisplayScrollingGraph
-
- doUpdate() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- doUpdateFMulti(int, IMoleculeList, CoordinatePairSet) - Method in class etomica.virial.ClusterSumMultibody
-
- doWait() - Method in class etomica.action.Activity
-
Method to put activity in a condition of being paused.
- doWheatley - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- doWheatley - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- doWiggle - Variable in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- doWiggle - Variable in class etomica.virial.simulations.SimulationVirial
-
- doWiggle - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- downList - Variable in class etomica.integrator.IntegratorHard
-
- downList - Variable in class etomica.nbr.list.AtomNeighborLists
-
- downList - Variable in class etomica.nbr.list.molecule.MoleculeNeighborLists
-
- dP - Variable in class etomica.normalmode.MeterSolidProps
-
- dP - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- dP - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- dPdRho(double) - Method in class etomica.modules.adsorption.EOSSWPatel
-
- dPdRho(double) - Method in class etomica.modules.adsorption.VEOS3SW
-
- dphi_du(int[], double[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- dphi_du(int[], double[]) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- dPlot - Variable in class etomica.modules.vle.B2Fit
-
- dPlot - Variable in class etomica.modules.vle.B2Fit.FunctionB2LJQ
-
- dPlot - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
-
- dpolx - Static variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- dpVirialOverlap - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- dqdVCalc(double, int) - Method in class etomica.veos.Ushcats
-
- dr - Variable in class etomica.association.AssociationHelperBranched
-
- dr - Variable in class etomica.association.AssociationHelperDouble
-
- dr - Variable in class etomica.association.AssociationHelperMolecule
-
- dr - Variable in class etomica.association.MCMoveAtomMonomer
-
- dr - Variable in class etomica.association.MCMoveAtomSmer
-
- dr - Variable in class etomica.association.MCMoveBiasUB
-
- dr - Variable in class etomica.association.MCMoveDimer
-
- dr - Variable in class etomica.association.MCMoveDimerRotate
-
- dr - Variable in class etomica.association.MCMoveMoleculeMonomer
-
- dr - Variable in class etomica.association.MCMoveMoleculeSmer
-
- dr - Variable in class etomica.association.MCMoveRotateAssociated
-
- dr - Variable in class etomica.association.MCMoveSmer
-
- dr - Variable in class etomica.association.MCMoveSmerRotate
-
- dr - Variable in class etomica.association.MCMoveVolumeAssociated
-
- dr - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- dr - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- dr - Variable in class etomica.data.meter.MeterRMSD
-
- dr - Variable in class etomica.data.meter.PotentialCalculationRDF
-
- dr - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- dr - Variable in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- dr - Variable in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- dr - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- dr - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
-
- dr - Variable in class etomica.graphics.ColorSchemeOverlap
-
- dr - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- dr - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- dr - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- dr - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- dr - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- dr - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- dr - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- dr - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
- dr - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
- dr - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- dr - Variable in class etomica.mappedvirial.MeterMeanForce
-
- dr - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- dr - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- dr - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- dr - Variable in class etomica.meam.P2EAM
-
- dr - Variable in class etomica.meam.PotentialCuLREP
-
- dr - Variable in class etomica.meam.PotentialEAM
-
- dr - Variable in class etomica.meam.PotentialEAM_LS
-
- dR - Variable in class etomica.meam.PotentialEAM_LS
-
- dr - Variable in class etomica.meam.PotentialEFS
-
- dr - Variable in class etomica.models.water.P2Water4PSoft
-
- dr - Variable in class etomica.modules.colloid.MeterEnd2End
-
- dr - Variable in class etomica.modules.droplet.IntegratorDroplet
-
- dr - Variable in class etomica.modules.droplet.MeterDeformation
-
- dr - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- dr - Variable in class etomica.modules.interfacial.MeterOrientation
-
- dr - Variable in class etomica.modules.mu.P1MagicWall
-
- dr - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- dr - Variable in class etomica.modules.rheology.MeterEndToEnd
-
- dr - Variable in class etomica.modules.rheology.MeterNormalStress
-
- dr - Variable in class etomica.modules.rheology.MeterViscosity
-
- dr - Variable in class etomica.modules.sam.MeterTilt
-
- dr - Variable in class etomica.molecule.MoleculePositionGeometricCenterPBC
-
- dr - Variable in class etomica.nbr.CriterionPositionWall
-
- dr - Variable in class etomica.nbr.CriterionSimple
-
- dr - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- dr - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
-
- dr - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- dr - Variable in class etomica.normalmode.MCMoveVolumeSolid
-
- dr - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- dr - Variable in class etomica.normalmode.MeterDADB
-
- dr - Variable in class etomica.normalmode.MeterDisplacementMoleculeRMS
-
- dr - Variable in class etomica.normalmode.MeterDisplacementRMS
-
- dr - Variable in class etomica.normalmode.MeterMaxExpansion
-
- dr - Variable in class etomica.normalmode.MeterPhiDeviation
-
- dr - Variable in class etomica.normalmode.MeterSolidDA
-
- dr - Variable in class etomica.normalmode.MeterSolidMirror
-
- dr - Variable in class etomica.normalmode.MeterSolidProps
-
- dr - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- dr - Variable in class etomica.normalmode.MeterThetaDeviation
-
- dr - Variable in class etomica.normalmode.MeterTilt
-
- dr - Variable in class etomica.normalmode.MeterTiltHistogram
-
- dr - Variable in class etomica.normalmode.MeterTiltRotation
-
- dr - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- dr - Variable in class etomica.normalmode.MeterTiltRotationStdev
-
- dr - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- dr - Variable in class etomica.normalmode.P2XOrder
-
- dr - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- dr - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- dr - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
-
- dr - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
-
- dr - Variable in class etomica.potential.P2HydrogenHinde
-
- dr - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- dr - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- dr - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- dr - Variable in class etomica.potential.P2HydrogenPatkowski
-
- dr - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- dr - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- dr - Variable in class etomica.potential.P2MoleculeTruncated
-
- dr - Variable in class etomica.potential.P2O2Bartolomei.P2O2TI
-
- dr - Variable in class etomica.potential.P2ReactionFieldDipole
-
- dr - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- dr - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- dr - Variable in class etomica.potential.P2SoftTruncated
-
- dr - Variable in class etomica.potential.P2SpheroPolyhedron
-
- dr - Variable in class etomica.potential.P3HydrogenATM
-
- dR - Variable in class etomica.potential.P3HydrogenGarberoglioMolecular
-
- dr - Variable in class etomica.potential.Potential2HardSpherical
-
- dr - Variable in class etomica.potential.Potential2SoftSpherical
-
- dr - Variable in class etomica.potential.Potential2SoftSphericalLS
-
- dr - Variable in class etomica.potential.PotentialCalculationPhiSum
-
- dr - Variable in class etomica.virial.CoordinatePairLeafSet
-
- dr - Variable in class etomica.virial.CoordinatePairMoleculeSet
-
- dr - Variable in class etomica.virial.MCMoveClusterAtomChainHSTail
-
- dr - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
-
- dr - Variable in class etomica.virial.MCMoveClusterAtomHSChain
-
- dr - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
-
- dr - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
-
- dr - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- dr - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
-
- dr0 - Variable in class etomica.models.water.P2Water4PSoft
-
- dr01 - Variable in class etomica.potential.P2Exp6
-
- dr01 - Variable in class etomica.potential.P2Exp6Buckingham
-
- dr01 - Variable in class etomica.potential.P2LennardJonesDreiding
-
- dr1 - Variable in class etomica.integrator.IntegratorGear4.Agent
-
- dr1 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- dr1 - Variable in class etomica.models.water.P2Water4PSoft
-
- dr1 - Variable in class etomica.potential.P3AxilrodTeller
-
- dr1 - Variable in class etomica.potential.P3Induction
-
- dr12 - Variable in class etomica.potential.P3BondAngle
-
- dr12 - Variable in class etomica.potential.P3BondAngleDreiding
-
- dr12 - Variable in class etomica.potential.P4TorsionDreiding
-
- dr2 - Variable in class etomica.association.MCMoveSmerRotate
-
- dr2 - Variable in class etomica.association.MCMoveVolumeAssociated
-
- dr2 - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- dr2 - Variable in class etomica.integrator.IntegratorGear4.Agent
-
- dr2 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- dr2 - Variable in class etomica.potential.P3AxilrodTeller
-
- dr2 - Variable in class etomica.potential.P3Induction
-
- dr21 - Variable in class etomica.potential.P4BondTorsion
-
- dr21 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- dr21 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- dr21 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- dr23 - Variable in class etomica.potential.P3BondAngle
-
- dr23 - Variable in class etomica.potential.P3BondAngleDreiding
-
- dr23 - Variable in class etomica.potential.P4BondTorsion
-
- dr23 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- dr23 - Variable in class etomica.potential.P4TorsionDreiding
-
- dr23 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- dr23 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- dr3 - Variable in class etomica.integrator.IntegratorGear4.Agent
-
- dr34 - Variable in class etomica.potential.P4BondTorsion
-
- dr34 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- dr34 - Variable in class etomica.potential.P4TorsionDreiding
-
- dr34 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- dr34 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- dr4 - Variable in class etomica.integrator.IntegratorGear4.Agent
-
- drA - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- drA - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- drA - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- dra - Variable in class etomica.potential.P4TorsionDreiding
-
- drAB - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- drAB - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- drAB - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- drAB - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- drAC - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- drAC - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- drAC - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- drAC - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- dragselected - Static variable in class org.jmol.script.Token
-
- drAll - Variable in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- draw() - Method in class etomica.graph.viewer.GraphMap
-
- draw(Graphics, int[], double) - Method in interface etomica.graphics.Drawable
-
- draw(Graphics, int[], double) - Method in class etomica.modules.osmosis.Osmosis.MyWall
-
- draw(Graphics, int[], double) - Method in class etomica.potential.P1HardBoundary
-
- draw(Graphics, int[], double) - Method in class etomica.potential.P1HardMovingBoundary
-
- draw() - Method in class g3dsys.control.G3DSys
-
- draw() - Method in class g3dsys.images.Axes
-
- draw() - Method in class g3dsys.images.Ball
-
- draw() - Method in class g3dsys.images.Bond
-
- draw() - Method in class g3dsys.images.Box
-
- draw() - Method in class g3dsys.images.Ellipse
-
- draw() - Method in class g3dsys.images.Figure
-
All Figures know how to draw themselves via override.
- draw() - Method in class g3dsys.images.ImageShell
-
- draw() - Method in class g3dsys.images.Line
-
- draw() - Method in class g3dsys.images.Triangle
-
- draw - Static variable in class org.jmol.script.Token
-
- draw(String, String, Point3f, float) - Method in class org.jmol.util.Quaternion
-
- DRAW_BOUNDARY_ALL - Static variable in class etomica.graphics.DisplayCanvas
-
- DRAW_BOUNDARY_MAX - Static variable in class etomica.graphics.DisplayCanvas
-
- DRAW_BOUNDARY_NONE - Static variable in class etomica.graphics.DisplayCanvas
-
- DRAW_BOUNDARY_OUTLINE - Static variable in class etomica.graphics.DisplayCanvas
-
- DRAW_BOUNDARY_SHELL - Static variable in class etomica.graphics.DisplayCanvas
-
- DRAW_EVERY_BOX - Static variable in class g3dsys.images.ImageShell
-
- DRAW_INNER_BOX - Static variable in class g3dsys.images.ImageShell
-
- DRAW_LARGE_BOX - Static variable in class g3dsys.images.ImageShell
-
- Drawable - Interface in etomica.graphics
-
- drawAtom(Graphics, int[], IAtom) - Method in class etomica.graphics.DisplayBoxCanvas2D
-
- drawAtom(Graphics, int[], IAtom) - Method in class etomica.graphics.DisplayBoxSpin2D
-
- drawAtom(Graphics, int[], IAtom) - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- drawBond(Point3f, Point3f, short, short, byte, short, int) - Method in class org.jmol.g3d.Graphics3D
-
- drawBonds - Variable in class etomica.modules.render.RenderMD.RenderMDParam
-
- drawDashedLine(int, int, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
-
- drawDottedLine(Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
-
- drawEllipse(Point3f, Point3f, Point3f, boolean, boolean) - Method in class org.jmol.g3d.Graphics3D
-
- drawFilledCircle(short, short, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- drawHermite4(int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
-
- drawHermite7(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int, short) - Method in class org.jmol.g3d.Graphics3D
-
- drawhover - Static variable in class org.jmol.script.Token
-
- drawImage(Object, Object, int, int, int, int) - Method in interface org.jmol.api.ApiPlatform
-
- drawImage(Object, Object, int, int, int, int) - Method in class org.jmol.awt.Platform
-
- drawImage(Object, int, int, int, int, short, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- drawImageToBuffer(Object, Object, Object, int, int, int) - Method in interface org.jmol.api.ApiPlatform
-
- drawImageToBuffer(Object, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
-
- drawLine(short, short, int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- drawLineAB(Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
-
- drawLineList - Variable in class etomica.graphics.DisplayPlot
-
- drawLineXYZ(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- drawpicking - Static variable in class org.jmol.script.Token
-
- drawPixel(int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- drawPoints(int, int[], int) - Method in class org.jmol.g3d.Graphics3D
-
- drawQuadrilateral(short, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
-
- drawRect(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
draws a rectangle
- drawSize - Variable in class etomica.graphics.DisplayBox
-
Size of drawing region of central image, in pixels
- drawSize - Variable in class etomica.graphics.DisplayPolytope
-
Size of drawing region of central image, in pixels
- drawString(String, JmolFont, int, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
-
draws the specified string in the current font.
- drawStringNoSlab(String, JmolFont, int, int, int, short) - Method in class org.jmol.g3d.Graphics3D
-
draws the specified string in the current font.
- drawSurface(MeshSurface, short) - Method in class org.jmol.g3d.Graphics3D
-
- drawTriangle3C(Point3i, short, Point3i, short, Point3i, short, int) - Method in class org.jmol.g3d.Graphics3D
-
- drawTriangle3I(Point3i, Point3i, Point3i, int) - Method in class org.jmol.g3d.Graphics3D
-
- drB - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- drB - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- drb - Variable in class etomica.potential.P4TorsionDreiding
-
- drBC - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- drBC - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- drBC - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- drBC - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- drbxa - Variable in class etomica.potential.P4TorsionDreiding
-
- drho - Variable in class etomica.statmech.HardSphereSolid.EOSParams
-
- dri - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- dri - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- drij - Variable in class etomica.meam.PotentialCuLREP
-
- drij - Variable in class etomica.meam.PotentialEAM
-
- drij - Variable in class etomica.meam.PotentialEFS
-
- drij - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- drij - Variable in class etomica.models.co2.P2CO2Hellmann
-
- drij - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- drij - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- drij - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- drijRot - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- drijRot - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- drijRot - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- drijRot - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- drijRot - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- drik - Variable in class etomica.meam.PotentialCuLREP
-
- drik - Variable in class etomica.meam.PotentialEAM
-
- drik - Variable in class etomica.meam.PotentialEFS
-
- drivePH() - Method in class etomica.integrator.IntegratorGear4NPH
-
- drivePT() - Method in class etomica.integrator.IntegratorGear4NPH
-
- drj - Variable in class etomica.normalmode.P1ConstraintNbr
-
- drj - Variable in class etomica.normalmode.P1ConstraintNbrHcp
-
- drj - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- drj - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- drj_tmp - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- drjk - Variable in class etomica.meam.PotentialCuLREP
-
- drjk - Variable in class etomica.meam.PotentialEAM
-
- drjk - Variable in class etomica.meam.PotentialEFS
-
- drk - Variable in class etomica.normalmode.P1ConstraintNbr
-
- drk - Variable in class etomica.normalmode.P1ConstraintNbrHcp
-
- drLat - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- drLatTmp - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- drOld - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- drOO - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- drop(Parser.CommandVariable) - Method in class etomica.graph.engine.Interpreter
-
- Droplet - Class in etomica.modules.droplet
-
Mesoscale simulation for Droplet module.
- Droplet(Space) - Constructor for class etomica.modules.droplet.Droplet
-
- DropletAtomic - Class in etomica.modules.droplet
-
Atomic simulation for Droplet module.
- DropletAtomic(Space) - Constructor for class etomica.modules.droplet.DropletAtomic
-
- DropletAtomicGraphic - Class in etomica.modules.droplet
-
Graphic UI for Droplet module.
- DropletAtomicGraphic(DropletAtomic, Space) - Constructor for class etomica.modules.droplet.DropletAtomicGraphic
-
- DropletAtomicGraphic.Applet - Class in etomica.modules.droplet
-
- DropletAtomicGraphic.DataSourceVaporDensity - Class in etomica.modules.droplet
-
- DropletGraphic - Class in etomica.modules.droplet
-
Graphic UI for Droplet module.
- DropletGraphic(Droplet, Space) - Constructor for class etomica.modules.droplet.DropletGraphic
-
- DropletGraphic.Applet - Class in etomica.modules.droplet
-
- DropletGraphic.DataProcessorTensorSplitter - Class in etomica.modules.droplet
-
Inner class to find the total pressure of the system from the pressure
tensor.
- DropletGraphic.ModifierBoxSize - Class in etomica.modules.droplet
-
- DropOrphanNodes - Class in etomica.graph.operations
-
- DropOrphanNodes() - Constructor for class etomica.graph.operations.DropOrphanNodes
-
- dropPrime() - Method in class etomica.veos.bigdecimal.Ifactor
-
Divide through the highest possible power of the highest prime.
- dropRadius - Variable in class etomica.modules.droplet.DropletAtomic
-
- drPrev - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- drSite0 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- drSite0 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- drSite1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- drSite1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- drSum - Variable in class etomica.modules.sam.MeterTilt
-
- drSum - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- drSum - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- drSum - Variable in class etomica.normalmode.MeterPlaneSlip
-
- drSum - Variable in class etomica.normalmode.MeterTilt
-
- drSum - Variable in class etomica.normalmode.MeterTiltRotation
-
- drSum - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- drSumPlane - Variable in class etomica.normalmode.MeterTiltRotation
-
- drSumSave - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- drTmp - Variable in class etomica.data.meter.MeterRMSD
-
- drTmp - Variable in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- drTmp - Variable in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- drtmp - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- drTmp - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- drtmp - Variable in class etomica.meam.PotentialEAM_LS
-
- dRtmp - Variable in class etomica.meam.PotentialEAM_LS
-
- drTmp - Variable in class etomica.potential.EwaldSummation
-
- drtmp - Variable in class etomica.potential.Potential2SoftSphericalLS
-
- drTot - Variable in class etomica.modules.colloid.MeterEnd2End
-
- drvDamp - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- ds - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- ds - Variable in class etomica.normalmode.MeterSolidMirror
-
- dSigma - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- dsmr - Variable in class etomica.normalmode.DataSourceAvgPressure2
-
- dss - Variable in class etomica.liquidLJ.LjMd3D.ValueCache
-
- dss - Variable in class etomica.liquidLJ.ValueCache
-
- dsspcalchydrogen - Static variable in class org.jmol.script.Token
-
- dst - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Destination image path.
- dst - Variable in class etomica.virial.CalcFFT
-
- dsum - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- dsum2 - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- dsvo - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- dsvo - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- dsvo - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- dsvo - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- dsvo - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- dsvo - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- dsvo - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- dsvo - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceChiSlope
-
- dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa
-
- dsvo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
-
- dsvo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- dsvo - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- dsvo - Variable in class etomica.normalmode.SimOverlap
-
- dsvo - Variable in class etomica.normalmode.SimOverlapLJ
-
- dsvo - Variable in class etomica.normalmode.SimOverlapLJModule
-
- dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- dsvo - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- dsvo - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- dsvo - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- dsvo - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- dTheta - Variable in class etomica.dimer.IntegratorDimerMin
-
- dTheta - Variable in class etomica.dimer.IntegratorDimerRT
-
- dTheta - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- dTheta - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- du(double) - Method in class etomica.models.rowley.P2RepRowley
-
The derivative r*du/dr.
- du(double) - Method in class etomica.modules.droplet.P2Cohesion
-
- du(double) - Method in class etomica.potential.P1HydrogenMielke
-
- du(double) - Method in interface etomica.potential.P1IntraMolecular
-
- du(double) - Method in class etomica.potential.P2Anharmonic
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2ArgonAziz1993
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2ArgonSlavicekEtAl2003
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2ArgonTangAndToennies2003
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
-
- du(double) - Method in class etomica.potential.P2Dreiding
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2Electrostatic
-
- du(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
- du(double) - Method in class etomica.potential.P2Exp6
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2Exp6Buckingham
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2Fene
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- du(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
- du(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
- du(double) - Method in class etomica.potential.P2Harmonic
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2HePCKLJS
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2HeSimplified
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
-
- du(double) - Method in class etomica.potential.P2Ideal
-
Returns zero.
- du(double) - Method in class etomica.potential.P2LennardJones
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2LennardJonesDreiding
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2LJQ
-
- du(double) - Method in class etomica.potential.P2LJQQ
-
- du(double) - Method in class etomica.potential.P2ModifiedMorse
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2Morse
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2QChemInterpolated
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2SoftSphere
-
The derivative r*du/dr.
- du(double) - Method in class etomica.potential.P2SoftSphericalTruncated
-
Returns the derivative (r du/dr) of the wrapped potential if the separation
is less than the cutoff value
- du(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
-
- du(double) - Method in class etomica.potential.P2SoftSphericalTruncatedForceShifted
-
- du(double) - Method in class etomica.potential.P2SoftTruncated
-
- du(double) - Method in class etomica.potential.P2WCA
-
The derivative r*du/dr.
- du(IAtomList) - Method in class etomica.potential.P4TorsionDreiding
-
- du(double) - Method in interface etomica.potential.Potential2Soft
-
The derivative of the pair energy, times the separation r: r du/dr.
- du(double) - Method in class etomica.potential.Potential2SoftSpherical
-
The derivative of the pair energy, times the separation r: r du/dr.
- du(double) - Method in class etomica.virial.P1IntraLambda
-
- du(double) - Method in class etomica.yukawa.P2HC2Yukawa
-
- du(double) - Method in class etomica.yukawa.P2Yukawa
-
r * du/dr method.
- dU_est - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- duCorrection(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
-
Uses result from integration-by-parts to evaluate integral of
r du/dr using integral of u.
- dUdcosphi(double) - Method in class etomica.potential.P4BondTorsion
-
- dudkT(double) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
-
- dUdphi(double) - Method in class etomica.potential.P4BondTorsionOPLS
-
- dudphi(int, double, double) - Static method in class etomica.potential.P4TorsionDreiding
-
- dUdRotA - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- dUdRotB - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- dummyRefCluster - Static variable in class etomica.virial.simulations.VirialN2
-
- dummyTarCluster - Static variable in class etomica.virial.simulations.VirialN2
-
- dumpArray(String, float[][], int, int, int, int) - Static method in class org.jmol.util.ArrayUtil
-
- dumpIntArray(int[], int) - Static method in class org.jmol.util.ArrayUtil
-
- dumpit - Variable in class etomica.overlap.DataOverlap
-
- dumpX - Variable in class etomica.metastable.DataProcessorXY
-
- dUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- dUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- dUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- dUnit - Variable in class etomica.modules.swmd.SwmdGraphic
-
- duWork - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- dv - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- dv - Variable in class etomica.association.BiasVolumeAceticAcid
-
- dV - Variable in class etomica.data.meter.MeterProfileByVolume
-
- dv - Variable in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- dv - Variable in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- dv - Variable in class etomica.integrator.IntegratorVelocityVerletRattle
-
- dv - Variable in class etomica.modules.catalysis.P2SquareWellBonding
-
- dv - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- dv - Variable in class etomica.modules.catalysis.P2SquareWellSurface
-
- dv - Variable in class etomica.modules.droplet.P2Cohesion
-
- dv - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- dv - Variable in class etomica.modules.mu.P1MagicWall
-
- dv - Variable in class etomica.modules.mu.P2SquareWellOneSide
-
- dv - Variable in class etomica.potential.P2DoubleWell
-
- dv - Variable in class etomica.potential.P2HardSphere
-
- dv - Variable in class etomica.potential.P2PenetrableSphere
-
- dv - Variable in class etomica.potential.P2PenetrableSquareWell
-
- dv - Variable in class etomica.potential.P2SquareWell
-
- dv - Variable in class etomica.potential.P2SquareWellRobust
-
- dv1 - Variable in class etomica.integrator.IntegratorGear4.Agent
-
- dv2 - Variable in class etomica.integrator.IntegratorGear4.Agent
-
- dv3 - Variable in class etomica.integrator.IntegratorGear4.Agent
-
- dv4 - Variable in class etomica.integrator.IntegratorGear4.Agent
-
- dvo - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- dvOO - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- dvTmp - Variable in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- dvTmp - Variable in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- dXl - Variable in class etomica.dimer.IntegratorDimerRT
-
- dy - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- dy - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- dy12 - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- dynamicmeasurements - Static variable in class org.jmol.script.Token
-
- Dyne - Class in etomica.units
-
The dyne unit of force, equal to 1 g-cm/s^2.
- G - Variable in class etomica.math.Gamma
-
- g - Variable in class etomica.modules.droplet.P1Smash
-
- G - Static variable in class etomica.util.Constants
-
The gravitational constant, in simulation units.
- g - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- g1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- G1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- g1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- G1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- g1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- G2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- g2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- G2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- g2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- G2pBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- G3Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- g3Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- G3DSys - Class in g3dsys.control
-
Abstraction and delegation container class to facilitate communication
between the CoordMapper, FigureManager, and G3DPanel without deeply
coupling them in their own definitions.
- G3DSys(Container) - Constructor for class g3dsys.control.G3DSys
-
- g3dsys.control - package g3dsys.control
-
- g3dsys.images - package g3dsys.images
-
- G3pBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- G4Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- g4Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- G_EARTH - Static variable in class etomica.util.Constants
-
The standard acceleration of gravity on Earth.
- ga - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- ga - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- gamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal
-
- gamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- Gamma - Class in etomica.math
-
This class calculates the incomplete gamma function and complementary
incomplete gamma function.
- Gamma() - Constructor for class etomica.math.Gamma
-
- gamma(double) - Static method in class etomica.math.SpecialFunctions
-
Returns the value of the gamma function of x.
- gamma() - Method in class etomica.meam.PotentialMEAM
-
- gamma - Variable in class etomica.models.co2.PNCO2GCPM
-
- gamma - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
-
- gamma - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- gamma - Variable in class etomica.models.water.PNWaterGCPM
-
- gamma - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- gamma(MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Euler-Mascheroni constant.
- Gamma(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The Gamma function.
- Gamma(Rational, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The Gamma function.
- gamma_New - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- gamma_New - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- gamma_Old - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- gamma_Old - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- gammai - Variable in class etomica.dimer.IntegratorDimerRT
-
- gb - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- gb - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- gbConst - Variable in class etomica.modules.clustergenerator.MyApplet
-
- gbLayout - Variable in class etomica.modules.clustergenerator.MyApplet
-
- GBond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- GBond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- GBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- gcd(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor
-
Greatest common divisor of this and oth.
- gComp - Variable in class etomica.graph.operations.BiComponentSubst.BiComponentSubstParameters
-
- gComp - Variable in class etomica.graph.operations.ComponentSubst.ComponentSubstParameters
-
- GCPMAgent(double, double, double, double, double, double, double, double) - Constructor for class etomica.models.co2.PNGCPM.GCPMAgent
-
- GCPMAgent(double, double, double, double, double, double, double, double, double) - Constructor for class etomica.models.co2.PNGCPM.GCPMAgent
-
- GData - Class in org.jmol.util
-
- GData() - Constructor for class org.jmol.util.GData
-
- geAtomPositionDefinition() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
- GEMCWithRotation - Class in etomica.simulation.prototypes
-
Simple Gibbs-ensemble Monte Carlo simulation of rotating molecules.
- GEMCWithRotation() - Constructor for class etomica.simulation.prototypes.GEMCWithRotation
-
- GEMCWithRotation(Space) - Constructor for class etomica.simulation.prototypes.GEMCWithRotation
-
- generalizedCoord - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- generalizedCoord - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- generateConfigs(String, double) - Method in class etomica.dimer.SimDimerLJadatom
-
- generateConfigs(String, double) - Method in class etomica.dimer.SimDimerMEAMadatom
-
- generateConfigs(String, double) - Method in class etomica.dimer.SimDimerMEAMGB
-
- generateGraphicsCB - Variable in class etomica.modules.clustergenerator.MyApplet
-
- generateNewU(double[]) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- generator - Variable in class etomica.modules.clustergenerator.MyApplet
-
- Geodesic - Class in org.jmol.util
-
Consolidated Geodesic from dotsRenderer 3/19/07 Bob Hanson
Constructs a canonical geodesic sphere of unit radius.
- Geodesic() - Constructor for class org.jmol.util.Geodesic
-
- geosurface - Static variable in class org.jmol.script.Token
-
- gestureswipefactor - Static variable in class org.jmol.script.Token
-
- get(String) - Method in class etomica.compatibility.FeatureSet
-
- get(String) - Static method in class etomica.graph.view.rasterizer.Messages
-
- get(String, String) - Static method in class etomica.graph.view.rasterizer.Messages
-
- get(Object) - Method in class etomica.server.dao.DataStreamStore
-
- get(Object) - Method in class etomica.server.dao.SimulationStore
-
- get(Object) - Method in class etomica.util.collections.IndexMap
-
- get(int) - Method in class etomica.util.collections.IndexMap
-
- get(int) - Method in class org.jmol.util.BitSet
-
Returns the value of the bit with the specified index.
- get(int) - Method in class org.jmol.util.Int2IntHash
-
- get(Vector3f) - Method in class org.jmol.util.Matrix4f
-
Retrieves the translational components of this matrix.
- get2ndDerivative() - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
-
- get2ndDerivative() - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- get2ndDerivative() - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- get2ndDerivative(int) - Method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- get2ndDerivativeFile(double[][], String) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- get2ndDerivativeMoleculei(CoordinateDefinition, int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- get2ndDerivativeMoleculei(CoordinateDefinition, int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- get2SidedNormix(Vector3f, BitSet) - Static method in class org.jmol.util.Normix
-
- get3dProjection(Vector3f) - Method in class org.jmol.util.Quaternion
-
- getA() - Method in class etomica.association.MCMoveMoleculeSmer
-
- getA() - Method in class etomica.math.geometry.Plane
-
- getA() - Method in class etomica.math.numerical.PadeApproximation
-
- getA() - Method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- getA() - Method in class etomica.modules.pistoncylinder.PistonPlane
-
- getA() - Method in class etomica.modules.rheology.IntegratorPolymer
-
- getA() - Method in class etomica.modules.sam.WallPlane
-
- getA() - Method in class etomica.potential.P2Exp6
-
- getA(int) - Method in class etomica.potential.P2HeSimplified
-
Returns the ith parameter value
u = A0 * exp(-A1*r) - A2/r^6 - A3/r^X
where X = 10 if useC10 is true, X=8 otherwise
- getA() - Method in class etomica.potential.P2ModifiedMorse
-
- getA() - Method in class etomica.potential.P2Morse
-
- getA() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
-
- getAcceptanceProbability() - Method in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- getAcceptanceTarget() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
- getAccumulator() - Method in class etomica.graphics.DisplayTextBoxesCAE
-
Accessor method for the data source that generates the displayed value.
- getAccumulators() - Method in class etomica.data.DataTableAverages
-
Returns a clone of the accumulator array.
- getAccumulators() - Method in class etomica.virial.MeterVirialBDBin
-
- getAccumulators() - Method in class etomica.virial.overlap.DataSourceVirialOverlap
-
- getAccumulators() - Method in class etomica.virial.overlap.DataVirialOverlap
-
- getAccumulatorUpdateInterval() - Method in class etomica.data.DataTableAverages
-
- getAcQuantity(int, int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOS
-
- getAcQuantity(int, int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- getAction() - Method in class etomica.action.activity.ControllerEvent
-
- getAction() - Method in class etomica.graphics.DeviceButton
-
Returns the currently defined action associated with the button.
- getAction() - Method in class etomica.integrator.IntegratorAnalytic
-
- getAction() - Method in class etomica.integrator.IntegratorListenerAction
-
- getAction() - Method in class etomica.zeolite.DeviceButtonSingle
-
Returns the currently defined action associated with the button.
- getActionStatus(IAction) - Method in class etomica.action.activity.Controller
-
Returns the status of an action held by the controller.
- getActivityIntegrate() - Method in class etomica.normalmode.SimOverlapModule
-
- getActualStepFreq0() - Method in class etomica.virial.overlap.IntegratorOverlap
-
- getAddAnotherSpecies() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getAddPotential() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getAddPotential() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getAddSameSpecies() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getAddSpecies() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getAddSpecies1() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getAddSpecies2() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getAddSpecies3() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getADimension() - Method in class etomica.potential.P2Exp6
-
- getADimension() - Method in class etomica.potential.P2Exp6Buckingham
-
- getAdjustInterval() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
- getAdjustInterval() - Method in class etomica.overlap.IntegratorOverlap
-
- getAdjustStepSize() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
- getAelement() - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- getAgent(IAtom) - Method in class etomica.atom.AtomLeafAgentManager
-
Returns the agent associated with the given IAtom.
- getAgent(AtomType) - Method in class etomica.atom.AtomTypeAgentManager
-
Convenience method to return the agent the given AtomType.
- getAgent(Box) - Method in class etomica.box.BoxAgentManager
-
- getAgent(IMolecule) - Method in class etomica.molecule.MoleculeAgentManager
-
Returns the agent associated with the given IAtom.
- getAgent(ISpecies) - Method in class etomica.species.SpeciesAgentManager
-
Convenience method to return the agent the given AtomType.
- getAgentClass() - Method in class etomica.dimer.IntegratorEnergyMap
-
- getAgentClass() - Method in class etomica.graphics.BondListener
-
- getAgentClass() - Method in class etomica.graphics.ColorSchemeCollectiveAgent
-
- getAgentClass() - Method in class etomica.graphics.ColorSchemeRandom
-
- getAgentClass() - Method in class etomica.integrator.IntegratorRigidIterative
-
- getAgentClass() - Method in class etomica.paracetamol.ChargeAgentSourceParacetamol
-
- getAgentClass() - Method in class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
-
- getAgentManager() - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- getAgentManager() - Method in class etomica.modules.catalysis.InteractionTracker
-
- getAgentManager() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- getAgentManager() - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- getAgentManager() - Method in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- getAgentManager() - Method in class etomica.normalmode.HSNPT.ActionSummer
-
- getAgents() - Method in class etomica.atom.AtomLeafAgentManager
-
Get the agents map.
- getAgents() - Method in class etomica.atom.AtomTypeAgentManager
-
- getAgents() - Method in class etomica.box.BoxAgentManager
-
- getAgents() - Method in class etomica.molecule.MoleculeAgentManager
-
- getAgents() - Method in class etomica.species.SpeciesAgentManager
-
- getAlertMessage() - Method in class etomica.virial.GUI.models.ModelAlertMsgDialog
-
- getAlertMsgBoxController() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- getAlertMsgBoxSpeciesRemoval() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getAlign(int) - Method in class etomica.graphics.DisplayBox
-
- getAlign(int) - Method in class etomica.graphics.DisplayPolytope
-
- getAlkaneIndex() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getAlkaneIndex() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getAlkaneLength(int) - Method in class etomica.virial.GUI.models.ModelAlkaneLengthSelection
-
- getAlkaneLengthSelectionDM() - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- getAlkaneLengthSelectionView(int) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- getAlkaneSpheresSpecies(IMolecularModel_SpeciesFactory) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- getAllActions() - Method in interface etomica.action.ActionGroup
-
Returns all actions from this group.
- getAllActions() - Method in class etomica.action.ActionGroupSeries
-
- getAllActions() - Method in class etomica.action.activity.ActivityGroupParallel
-
- getAllActions() - Method in class etomica.action.activity.ActivityGroupSeries
-
- getAllCoordinates() - Method in class etomica.meta.wrappers.SimulationWrapper
-
Array of coordinates of all atoms in all boxes in the wrapped Simulation.
- getAllIdsOfType(Class) - Method in class etomica.meta.SimulationModel
-
- getAllLastValues(BoxCluster) - Method in interface etomica.virial.ClusterAbstractMultivalue
-
- getAllLastValues(BoxCluster) - Method in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- getAllLastValues(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- getAllLastValues(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- getAllLastValues(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
- getAllLastValues(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- getAllMyData() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- getAllMyData() - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- getAllMyData() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- getAllowedScriptTypes() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Returns the list of allowed script types.
- getAllQuantity(int, int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOS
-
- getAllQuantity(int, int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- getAllredRochowElectroNeg(int) - Static method in class org.jmol.util.Elements
-
- getAlpha() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- getAlpha() - Method in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
-
- getAlpha(int) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- getAlpha(int) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- getAlpha(int) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- getAlpha() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- getAlpha() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- getAlpha() - Method in class etomica.normalmode.MCMoveHarmonicEin
-
- getAlpha(int) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- getAlpha(int) - Method in class etomica.normalmode.MeterTargetTP
-
- getAlpha(int) - Method in interface etomica.overlap.AlphaSource
-
Returns the ith alpha value (i=0..(n-1))
- getAlpha(int) - Method in class etomica.overlap.MeterOverlap
-
- getAlpha() - Method in class etomica.potential.P2Dreiding
-
- getAlpha() - Method in class etomica.potential.P2Exp6Buckingham
-
- getAlpha(int) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
Returns ith factor used in the overlap value.
- getAlphaCarbonType() - Method in class etomica.models.rowley.SpeciesEthanol
-
- getAlphaCarbonType() - Method in class etomica.models.rowley.SpeciesMethanol
-
- getAlphaCenter() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- getAlphaCenter() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- getAlphaCenter() - Method in class etomica.normalmode.SimOverlapModule
-
- getAlphaCenter() - Method in class etomica.overlap.MeterOverlap
-
- getAlphaCenter() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- getAlphaCenter() - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- getAlphaFac() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- getAlphaHydrogenType() - Method in class etomica.models.rowley.SpeciesEthanol
-
- getAlphaHydrogenType() - Method in class etomica.models.rowley.SpeciesMethanol
-
- getAlphaSource() - Method in class etomica.overlap.DataOverlap
-
Returns an object capable of returning the different alpha values being
used.
- getAlphaSource() - Method in class etomica.virial.overlap.DataVirialOverlap
-
- getAlphaSpan() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- getAlphaSpan() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- getAlphaSpan() - Method in class etomica.overlap.MeterOverlap
-
- getAlphaSpan() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- getAlphaSpan() - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- getAlternateStylesheet() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getAlterSimEnv() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getAlterSimEnv() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getAmbientPercent() - Static method in class org.jmol.util.GData
-
- getAminoAcidValenceAndCharge(String, String, int[]) - Static method in class org.jmol.viewer.JmolConstants
-
returns an array if we have special hybridization or charge
- getAmplitude() - Method in class etomica.potential.P2Fene
-
- getAmplitudeDimension() - Method in class etomica.potential.P2Fene
-
Not implemented correctly.
- getAngle(int) - Method in class etomica.config.ConformationChainLinear
-
- getAngle(int) - Method in class etomica.config.ConformationLinear
-
- getAngle() - Method in class etomica.math.Quaternion
-
Returns the angle associated with the quaternion
- getAngle() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- getAngle() - Method in class etomica.potential.P3BondAngle
-
Returns the nominal bond angle (in radians)
- getAngle() - Method in class etomica.potential.P3BondAngleDreiding
-
Returns the nominal bond angle (in radians)
- getAngle() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
Returns the nominal bond angle (in radians)
- getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveCubic
-
- getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- getAngleAlpha() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveCubic
-
- getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- getAngleBeta() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- getAngleDimension() - Method in class etomica.potential.P3BondAngle
-
- getAngleDimension() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveCubic
-
- getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- getAngleGamma() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- getAngles() - Method in class etomica.potential.P2WaterPotentialsJankowski
-
- getAngstromDepth() - Method in class g3dsys.control.G3DSys
-
Gets the Angstrom depth of the model
- getAngstromHeight() - Method in class g3dsys.control.G3DSys
-
Gets the Angstrom height of the model
- getAngstromWidth() - Method in class g3dsys.control.G3DSys
-
Gets the Angstrom width of the model
- getAngularVelocity() - Method in class etomica.atom.AtomOrientedDynamic
-
- getAngularVelocity() - Method in interface etomica.atom.IAtomOrientedKinetic
-
- getAngularVelocity() - Method in interface etomica.molecule.IMoleculeOrientedKinetic
-
- getAngularVelocity() - Method in class etomica.molecule.MoleculeOrientedDynamic
-
- getAnharmonicConstant() - Method in class etomica.potential.P2Anharmonic
-
- getAnharmonicConstantDimension() - Method in class etomica.potential.P2Anharmonic
-
- getAPair(int, int) - Method in class etomica.virial.AtomPairSet
-
Returns atom pair for ith and jth atoms in set.
- getAPairSet() - Method in class etomica.virial.BoxCluster
-
- getApi1A() - Method in class etomica.molecule.iterator.MpiMolecule
-
Returns the 1A iterator set at construction.
- getApiAA() - Method in class etomica.molecule.iterator.MpiMolecule
-
Returns the AA iterator set at construction.
- getApproximation() - Method in class etomica.virial.cluster.ClusterOperations
-
- getArea() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getArea() - Method in class etomica.math.geometry.Parallelogram
-
- getArea() - Method in class etomica.math.geometry.Polygon
-
- getArea() - Method in class etomica.math.geometry.PolygonGeneral
-
Returns the value of the area enclosed by the polygon
- getArea() - Method in class etomica.math.geometry.Rectangle
-
Returns the area enclosed by the rectangle.
- getArea() - Method in class etomica.math.geometry.Square
-
Returns edgeLength^2.
- getArgb(short) - Static method in class org.jmol.util.Colix
-
- getArgb() - Method in class org.jmol.util.Rgb16
-
- getArgbFromString(String) - Static method in class org.jmol.util.ColorUtil
-
accepts [xRRGGBB] or [0xRRGGBB] or [0xFFRRGGBB] or #RRGGBB or
[red,green,blue] or a valid JavaScript color
- getArgbGreyscale(short) - Static method in class org.jmol.util.Colix
-
- getArray() - Method in class etomica.atom.AtomsetArray
-
- getArray() - Method in class etomica.molecule.MoleculesetArray
-
- getArrayDimension() - Method in class etomica.data.types.DataDoubleArray
-
Returns the dimension of the array, which is the number of integer
indices needed to access one of its elements.
- getArrayDimension() - Method in class etomica.data.types.DataDoubleBDArray
-
Returns the dimension of the array, which is the number of integer
indices needed to access one of its elements.
- getArrayList() - Method in class etomica.atom.AtomListWrapper
-
- getArrayList() - Method in class etomica.molecule.MoleculeListWrapper
-
- getArrayListPotentialCollection() - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- getArrayShape() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
-
Returns the size of each dimension in the constructed DataDoubleArray.
- getArrayShape() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory
-
Returns a copy of the array shape array.
- getArrayShape(int) - Method in class etomica.data.types.DataDoubleArray
-
Returns the length of the array in the i-th dimension.
- getArrayShape() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
-
Returns the size of each dimension in the constructed DataDoubleArray.
- getArrayShape() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
-
Returns a copy of the array shape array.
- getArrayShape(int) - Method in class etomica.data.types.DataDoubleBDArray
-
Returns the length of the array in the i-th dimension.
- getArticulationPair() - Method in class etomica.graph.property.FFTDecomposition
-
- getArticulationPair() - Method in class etomica.graph.property.IsFFT
-
- getArticulationPoints() - Method in class etomica.graph.property.HasSimpleArticulationPoint
-
- getAscent() - Method in class org.jmol.util.JmolFont
-
- getAspect() - Method in class g3dsys.images.Ellipse
-
set the aspect ratio (y/x) of the figure
- getAssociatedAtoms() - Method in class etomica.association.AssociationManager
-
- getAssociatedAtoms(IAtom) - Method in class etomica.association.AssociationManager
-
Returns the number of atoms on the list of associations of the given atom.
- getAssociatedMolecules() - Method in class etomica.association.AssociationManagerMolecule
-
- getAssociatedMolecules(IMolecule) - Method in class etomica.association.AssociationManagerMolecule
-
Returns the number of atoms on the list of associations of the given atom.
- getAssociationDefinition() - Method in class etomica.association.AssociationManager
-
- getAssociationDefinition() - Method in class etomica.association.AssociationManagerMolecule
-
- getAsText() - Method in class etomica.graphics.DimensionedDoubleEditor
-
Returns the value in the editor's units, formatted as a text string.
- getAtom() - Method in class etomica.association.AtomSourceRandomDimer
-
- getAtom() - Method in class etomica.association.AtomSourceRandomMonomer
-
- getAtom() - Method in class etomica.association.AtomSourceRandomSmer
-
- getAtom(int) - Method in class etomica.atom.AtomArrayList
-
- getAtom(int) - Method in class etomica.atom.AtomListWrapper
-
Part of implementation of AtomSet interface.
- getAtom(int) - Method in class etomica.atom.AtomPair
-
- getAtom(int) - Method in class etomica.atom.AtomsetArray
-
Part of implementation of AtomSet interface.
- getAtom(int) - Method in class etomica.atom.AtomSetSinglet
-
- getAtom() - Method in interface etomica.atom.AtomSource
-
Returns an atom.
- getAtom() - Method in class etomica.atom.AtomSourceRandomLeaf
-
returns a random atom from the box's leaf atom list
- getAtom() - Method in class etomica.atom.AtomSourceRandomSpecies
-
returns a random atom from the box's leaf atom list
- getAtom(int) - Method in interface etomica.atom.IAtomList
-
Returns the i-th atom, with numbering beginning from 0.
- getAtom() - Method in class etomica.atom.iterator.AtomIteratorSinglet
-
- getAtom() - Method in class etomica.box.BoxAtomEvent
-
- getAtom() - Method in class etomica.graphics.ColorSchemeNeighbor
-
- getAtom() - Method in class etomica.graphics.ColorSchemeNeighborCell
-
- getAtom() - Method in class etomica.nbr.site.AtomSite
-
- getAtom() - Method in class etomica.potential.PotentialReactive.BondChangeData
-
- getAtom_aC_A() - Method in class etomica.action.IntegratorDimerApproach
-
- getAtom_aC_B() - Method in class etomica.action.IntegratorDimerApproach
-
- getAtom_aH_A() - Method in class etomica.action.IntegratorDimerApproach
-
- getAtom_aH_B() - Method in class etomica.action.IntegratorDimerApproach
-
- getAtom_H1_A() - Method in class etomica.action.IntegratorDimerApproach
-
- getAtom_O_A() - Method in class etomica.action.IntegratorDimerApproach
-
- getAtom_O_B() - Method in class etomica.action.IntegratorDimerApproach
-
- getAtomAction() - Method in class etomica.action.MoleculeChildAtomAction
-
- getAtomAgentManager() - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- getAtomColor(IAtom) - Method in class etomica.association.ColorSchemeSmer
-
- getAtomColor(IAtom) - Method in class etomica.association.ColorSchemeSmerByLength
-
- getAtomColor(IAtom) - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- getAtomColor(IAtom) - Method in class etomica.graphics.ColorScheme
-
- getAtomColor(IAtom) - Method in class etomica.graphics.ColorScheme.Simple
-
- getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeByType
-
- getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeCell
-
- getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeCollectiveAgent
-
- getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeColliders
-
Applies the special colors to the colliding pair while coloring all other atoms with baseColor.
- getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeNull
-
Return without changing atom's color.
- getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeRandom
-
- getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeRandomByMolecule
-
- getAtomColor(IAtom) - Method in class etomica.graphics.ColorSchemeTemperature
-
- getAtomColor(IAtom) - Method in class etomica.modules.catalysis.ColorSchemeRadical
-
- getAtomColor(IAtom) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- getAtomColor(IAtom) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
-
- getAtomColor(IAtom) - Method in class etomica.modules.crystalviewer.ColorSchemePlane
-
- getAtomColor(IAtom) - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
-
- getAtomColor(IAtom) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- getAtomColor(IAtom) - Method in class etomica.modules.materialfracture.StrainColorScheme
-
- getAtomColor(IAtom) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- getAtomCount() - Method in class etomica.atom.AtomArrayList
-
- getAtomCount() - Method in class etomica.atom.AtomListWrapper
-
Returns the length of the wrapped array.
- getAtomCount() - Method in class etomica.atom.AtomPair
-
- getAtomCount() - Method in class etomica.atom.AtomsetArray
-
Returns the length of the wrapped array.
- getAtomCount() - Method in class etomica.atom.AtomSetSinglet
-
- getAtomCount() - Method in interface etomica.atom.IAtomList
-
- getAtomDataInfo() - Method in interface etomica.data.DataSourceAtomic
-
- getAtomDataInfo() - Method in class etomica.data.DataSourceRmsVelocity
-
- getAtomDataInfo() - Method in class etomica.data.meter.MeterTensorVelocity
-
- getAtomFilter() - Method in class etomica.graphics.DisplayBox
-
Accessor method for the atom filter that determines which atoms
are displayed.
- getAtomicAndIsotopeNumber(int, int) - Static method in class org.jmol.util.Elements
-
- getAtomicMass(int) - Static method in class org.jmol.util.Elements
-
- getAtomicNumber() - Method in class etomica.chem.elements.ElementChemical
-
- getAtomicNumberDimension() - Method in class etomica.chem.elements.ElementChemical
-
- getAtomLeaf1(Box) - Static method in class etomica.util.Debug
-
Returns an AtomPair containing the two atoms with global indices
ATOM1_INDEX and ATOM2_INDEX within the given box.
- getAtomList(IAtom) - Method in interface etomica.atom.AtomToAtomLeafList
-
Returns the ArrayList that this instance associates with the given atom.
- getAtomList(IAtom) - Method in class etomica.atom.AtomToAtomSetFixed
-
- getAtomList(IAtom) - Method in class etomica.atom.AtomToParentChildList
-
- getAtomPositionDefinition() - Method in class etomica.action.MoleculeActionTranslateTo
-
- getAtomPositionDefinition() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- getAtomPropertiesLike(String) - Static method in class org.jmol.script.Token
-
- getAtoms() - Method in interface etomica.atom.IAtomList
-
- getAtoms(Box) - Static method in class etomica.util.Debug
-
Returns an AtomPair containing the two atoms with global indices
ATOM1_INDEX and ATOM2_INDEX within the given box.
- getAtomSource() - Method in class etomica.association.MCMoveDimer
-
- getAtomSource() - Method in class etomica.association.MCMoveDimerRotate
-
- getAtomSource() - Method in class etomica.association.MCMoveSmer
-
- getAtomSource() - Method in class etomica.association.MCMoveSmerRotate
-
- getAtomSource() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- getAtomSource() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- getAtomSource() - Method in class etomica.integrator.mcmove.MCMoveAtom
-
The AtomSource is used to select the atom at the beginning of the trial
- getAtomSource() - Method in class etomica.integrator.mcmove.MCMoveDimer
-
- getAtomSource() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- getAtomSource() - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
- getAtomSource() - Method in class etomica.models.hexane.MCMoveReptate
-
- getAtomSource() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- getAtomSource() - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- getAtomSource() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- getAtomSource() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- getAtomSource() - Method in class etomica.virial.MCMoveClusterAngleBend
-
- getAtomSource() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- getAtomSource() - Method in class etomica.virial.MCMoveClusterAtomQ
-
- getAtomType() - Method in class etomica.simulation.SimulationAtomTypeEvent
-
- getAtomType(int) - Method in interface etomica.species.ISpecies
-
Returns the child types of this group for the specified index.
- getAtomType(int) - Method in class etomica.species.Species
-
- getAtomTypeCount() - Method in interface etomica.species.ISpecies
-
Returns the number of child types of this group.
- getAtomTypeCount() - Method in class etomica.species.Species
-
- getAtomTypes(IPotential) - Method in class etomica.potential.PotentialGroup
-
Returns the AtomTypes that the given potential applies to if the given
potential is within this potential group.
- getAtomTypes() - Method in interface etomica.species.ISpecies
-
Get the list of AtomTypes that make up this Species.
- getAtomTypes() - Method in class etomica.species.Species
-
- getAverage(int) - Method in interface etomica.overlap.DataOverlap.DataSourceOverlapAvg
-
- getAverage(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
-
- getAverage(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgSimple
-
- getAverage(int) - Method in class etomica.overlap.DataOverlap
-
Returns the ratio of the reference to target overlap ratio
reference/target for the given value alpha.
- getAverage(int) - Method in class etomica.virial.overlap.DataSourceVirialOverlap
-
Returns the ratio of the reference to target overlap-to-virial ratios
(which reduces to target/reference) for the given value of the Bennet
parameter.
- getAverageAndError(int, double, boolean) - Method in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
-
- getAverageAndError(double) - Method in class etomica.overlap.DataOverlap
-
Returns the average ratio and its uncertainty for the given value of
alpha
- getAverageAndError(boolean, double) - Method in class etomica.overlap.DataOverlap
-
Returns the average from the reference or target system (as specified)
and its uncertainty for the given value of alpha
- getAverageAndError(int, double, boolean) - Method in class etomica.overlap.DataOverlap
-
- getAverageAndError() - Method in class etomica.virial.overlap.DataVirialOverlap
-
Returns the total result (appropriate ratio of target, reference and
overlap averages) and the uncertainty on that value.
- getAverageAndError(int) - Method in class etomica.virial.overlap.DataVirialOverlap
-
- getAverageAntibiasedLogs() - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
-
Returns the average natural logs of the block averages, for all block
sizes.
- getAverageAtomPoint() - Method in class g3dsys.control.G3DSys
-
- getAverageLogs() - Method in class etomica.data.AccumulatorAverageBootstrap
-
Returns the average natural logs of the block averages, for all block
sizes.
- getAverageLogs() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Returns the average natural logs of the block averages, for all block
sizes.
- getAverages() - Method in class etomica.data.AccumulatorAverageBootstrap
-
Returns the averages for all block sizes
- getAverages() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Returns the averages for all block sizes
- getAvg() - Method in class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- getAvg(int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- getAvgBondLength(double) - Static method in class etomica.atom.AtomHydrogen
-
- getAvgDouble() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- getAxesForEllipsoid(double[], Vector3f[], float[]) - Static method in class org.jmol.util.Quadric
-
- getAxis() - Method in class etomica.math.Quaternion
-
Returns the axis associated with the Quaternion.
- getB() - Method in class etomica.association.MCMoveBiasUB
-
- getB() - Method in class etomica.math.geometry.Plane
-
- getB() - Method in class etomica.math.numerical.PadeApproximation
-
- getB() - Method in class etomica.modules.pistoncylinder.PistonPlane
-
- getB() - Method in class etomica.modules.rheology.IntegratorPolymer
-
- getB() - Method in class etomica.modules.sam.P1Sinusoidal
-
- getB() - Method in class etomica.modules.sam.WallPlane
-
- getB() - Method in class etomica.potential.P2Exp6
-
- getB(int) - Method in class etomica.virial.cluster.ClusterOperations
-
- getB() - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- getBackgroundColor() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getBackgroundColor() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Gets the background color of the display box canvas.
- getBackgroundColor() - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Gets the background color of the display box canvas.
- getBarrier() - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- getBarrier() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- getBarrier() - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
-
- getBarrierDimension() - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
-
- getBasis() - Method in class etomica.lattice.BravaisLatticeCrystal
-
- getBasis() - Method in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- getBasis() - Method in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- getBasis() - Method in class etomica.normalmode.CoordinateDefinition
-
- getBasisCells() - Method in class etomica.normalmode.CoordinateDefinition
-
- getBasisMolecules() - Method in class etomica.modules.sam.ConfigurationSAM
-
- getBasisSize() - Method in class etomica.lattice.LatticeCubicSimple
-
Returns 1.
- getBasisSurface() - Method in class etomica.modules.sam.ConfigurationSAM
-
- getBboxVertices() - Method in class org.jmol.util.BoxInfo
-
- getBDimension() - Method in class etomica.potential.P2Exp6
-
- getBDimension() - Method in class etomica.potential.P2Exp6Buckingham
-
- getBennetAverage(int) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
Returns average value of expression used to determine optimal
Bennet parameter (value[1]/(value[1]+expX[iParam]).
- getBennetBias(int) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
Returns iParam'th factor used in the Bennet sum.
- getBennetBias(int) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
Returns iParam'th factor used in the Bennet sum.
- getBeta() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- getBeta() - Method in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
-
- getBeta() - Method in class etomica.potential.P4TorsionDreiding
-
- getBetaUAWf() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- getBetaUAWf() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- getBetaUAWr() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- getBetaUAWr() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- getBetaUBWf() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- getBetaUBWf() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- getBetaUBWr() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- getBetaUBWr() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- getBgColixes(short[]) - Method in class org.jmol.util.GData
-
- getBiasCubeDimensions() - Method in class etomica.association.BiasVolumeCube
-
- getBiasSphereRadius() - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- getBiasSphereRadius() - Method in class etomica.association.BiasVolumeAceticAcid
-
- getBiasSphereRadius() - Method in class etomica.association.BiasVolumeSphere
-
- getBiasSphereRadius() - Method in class etomica.association.BiasVolumeSphereOriented
-
- getBiasSphereRadius() - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
- getBiComponents(Graph) - Static method in class etomica.graph.traversal.BCVisitor
-
Returns the biconnected components of the given graph.
- getBinCounts() - Method in class etomica.data.histogram.HistogramSimple
-
- getBinSize() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- getBisectingPlane(Point3f, Vector3f, Point3f, Vector3f, Point4f) - Static method in class org.jmol.util.Measure
-
- getBitSet(ScriptVariable, boolean) - Static method in class org.jmol.script.ScriptVariable
-
- getBlockCount() - Method in class etomica.data.AccumulatorAverage
-
- getBlockDataSink() - Method in class etomica.data.AccumulatorAverageFixed
-
- getBlockingSet(Graph) - Method in class etomica.graph.iterators.filters.GlobalFilter
-
- getBlockSize() - Method in class etomica.data.AccumulatorAverage
-
- getBn(double, double[], double[]) - Static method in class etomica.virial.BnJHBVArgon_Analytic
-
- getBond(IAtom) - Method in class etomica.potential.P2HardBondedList.BondArrayList
-
- getBond(int) - Method in class etomica.virial.cluster.ClusterCollapsedTreeNode
-
- getBond(int) - Method in class etomica.virial.cluster.ClusterTreeNode
-
- getBondAngle() - Method in class etomica.models.hexane.SpeciesHexane
-
- getBondChangeData() - Method in interface etomica.potential.PotentialReactive
-
- getBondConstratins(ISpecies) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- getBondDelta() - Method in class etomica.potential.P2HardBond
-
Accessor method for the bond extension factor
- getBondDelta() - Method in class etomica.potential.P2PenetrableBond
-
Accessor method for the bond extension factor
- getBondedList(IAtom) - Method in class etomica.potential.P2HardBondedList
-
Returns the list containing the bonds for the given atom.
- getBondFac() - Method in class etomica.modules.colloid.P2HardSphereMC
-
- getBondFac() - Method in class etomica.modules.colloid.P2SquareWellMonomer
-
- getBondIndexArray() - Method in class etomica.virial.ClusterBonds
-
- getBondingPotential() - Method in class etomica.chem.models.ModelChain
-
Returns the bonding potential used for adjacent atoms in the chain
molecule.
- getBondingRadFromTable(int, int, short[]) - Static method in class org.jmol.util.Elements
-
- getBondingRadiusFloat(short, int) - Static method in class org.jmol.util.Elements
-
- getBondL() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getBondL() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getBondL() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getBondL() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getBondL() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getBondL() - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- getBondL() - Method in class etomica.virial.SpeciesFactorySpheres2
-
- getBondLength() - Method in class etomica.atom.AtomHydrogen
-
- getBondLength() - Method in class etomica.config.ConformationChainLinear
-
- getBondLength() - Method in class etomica.config.ConformationLinear
-
- getBondlength() - Method in class etomica.models.hexane.CBMCGrowSolidHexane
-
- getBondLength() - Method in class etomica.models.hexane.SpeciesHexane
-
- getBondLength() - Method in class etomica.potential.P2Dreiding
-
- getBondLength() - Method in class etomica.potential.P2HardBond
-
Accessor method for the bond length
- getBondLength() - Method in class etomica.potential.P2PenetrableBond
-
Accessor method for the bond length
- getBondLength() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getBondLength() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getBondLength() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getBondLengthDimension() - Method in class etomica.config.ConformationChainLinear
-
- getBondLengthDimension() - Method in class etomica.config.ConformationLinear
-
- getBondLengthDimension() - Method in class etomica.potential.P2HardBond
-
- getBondLengthDimension() - Method in class etomica.potential.P2PenetrableBond
-
- getBondLengths() - Method in class etomica.potential.P2WaterPotentialsJankowski
-
- getBondsTree() - Method in class etomica.virial.ClusterTree
-
- getBondTheta() - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- getBondTheta() - Method in class etomica.virial.SpeciesFactorySpheres2
-
- getBondType() - Method in class g3dsys.images.Bond
-
- getBoolean() - Method in class etomica.integrator.IntegratorGear4NPH.EnsembleToggler
-
- getBoolean() - Method in interface etomica.modifier.ModifierBoolean
-
Returns the current state of the modified value.
- getBoolean() - Method in class etomica.modules.joulethomson.IntegratorJT.EnsembleToggler
-
- getBoolean(boolean) - Static method in class org.jmol.script.ScriptVariable
-
- getBoundaries() - Method in class etomica.modules.rosmosis.MeterFlux
-
- getBoundary() - Method in class etomica.box.Box
-
- getBoundary() - Method in class etomica.space.BoundaryEvent
-
- getBoundaryFrameColor() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Gets the color of box boundary.
- getBoundaryFrameColor() - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Gets the color of box boundary.
- getBoundaryPadding() - Method in class etomica.config.ConfigurationLattice
-
- getBoundaryTensor() - Method in class etomica.space.BoundaryDeformablePeriodic
-
Returns the boundary tensor that fully describes the shape of the boundary.
- getBoundaryVectors() - Method in class g3dsys.control.G3DSys
-
Gets the boundary vectors used for calculating image shells
- getBoundaryVectors() - Method in class g3dsys.images.ImageShell
-
- getBoundaryVectorsIterator() - Method in class g3dsys.control.G3DSys
-
Gets the index iterator used for calculating image shells
- getBoundaryVectorsIterator() - Method in class g3dsys.images.ImageShell
-
- getBoundBoxCenter() - Method in class org.jmol.util.BoxInfo
-
- getBoundBoxCornerVector() - Method in class org.jmol.util.BoxInfo
-
- getBoundBoxInfo() - Method in class org.jmol.util.BoxInfo
-
- getBoundBoxPoints(boolean) - Method in class org.jmol.util.BoxInfo
-
- getBoundingBoxCenter() - Method in class g3dsys.control.G3DSys
-
- getBox() - Method in class etomica.action.ActionMinimizeEnergy
-
- getBox() - Method in interface etomica.action.BoxAction
-
- getBox() - Method in class etomica.action.BoxActionAdapter
-
- getBox() - Method in class etomica.action.BoxRandomizeMomenta
-
- getBox() - Method in class etomica.action.BoxScaleMomenta
-
- getBox() - Method in class etomica.action.WriteConfiguration
-
Returns the box whose atom coordinates get written to the file.
- getBox() - Method in class etomica.action.WriteConfigurationBinary
-
Returns the box whose atom coordinates get written to the file.
- getBox() - Method in class etomica.action.WriteConfigurationDLPOLY
-
Returns the box whose atom coordinates get written to the file.
- getBox() - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
Returns the box whose atom coordinates get written to the file.
- getBox() - Method in class etomica.association.MeterDimerMoleFraction
-
- getBox() - Method in class etomica.atom.AtomLeafAgentManager
-
Convenience method to return the box the Manager is tracking.
- getBox() - Method in class etomica.box.BoxEvent
-
- getBox() - Method in class etomica.data.DataProcessorInterfacialTension
-
- getBox() - Method in class etomica.data.meter.MeterAvgBondLength
-
- getBox() - Method in class etomica.data.meter.MeterDensity
-
- getBox() - Method in class etomica.data.meter.MeterDihedralAngle
-
- getBox() - Method in class etomica.data.meter.MeterDipoleSumSquared1site
-
- getBox() - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- getBox() - Method in class etomica.data.meter.MeterDipoleSumSquaredTIP4PWater
-
- getBox() - Method in class etomica.data.meter.MeterKineticEnergy
-
- getBox() - Method in class etomica.data.meter.MeterKineticEnergyRigid
-
- getBox() - Method in class etomica.data.meter.MeterLocalMoleFraction
-
- getBox() - Method in class etomica.data.meter.MeterMoleFraction
-
- getBox() - Method in class etomica.data.meter.MeterMomentumCOM
-
- getBox() - Method in class etomica.data.meter.MeterNMolecules
-
- getBox() - Method in class etomica.data.meter.MeterPositionCOM
-
- getBox() - Method in class etomica.data.meter.MeterPotentialEnergy
-
- getBox() - Method in class etomica.data.meter.MeterPressureTensor
-
Returns the integrator associated with this instance.
- getBox() - Method in class etomica.data.meter.MeterProfile
-
- getBox() - Method in class etomica.data.meter.MeterProfileByAtoms
-
- getBox() - Method in class etomica.data.meter.MeterProfileByVolume
-
- getBox() - Method in class etomica.data.meter.MeterRadiusGyration
-
- getBox() - Method in class etomica.data.meter.MeterRDF
-
- getBox() - Method in class etomica.data.meter.MeterRDFPC
-
- getBox() - Method in class etomica.data.meter.MeterTensorVelocity
-
- getBox() - Method in class etomica.data.meter.MeterVolume
-
- getBox() - Method in class etomica.graphics.DeviceNSelector
-
- getBox() - Method in class etomica.graphics.DisplayBox
-
- getBox() - Method in class etomica.integrator.IntegratorBox
-
- getBox() - Method in class etomica.integrator.mcmove.MCMoveBox
-
- getBox() - Method in class etomica.integrator.mcmove.MCMoveManager
-
- getBox() - Method in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- getBox() - Method in class etomica.mappedRdf.MeterMappedRdf
-
- getBox() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- getBox() - Method in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- getBox() - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- getBox() - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- getBox() - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- getBox() - Method in class etomica.modules.dcvgcmd.MeterFlux
-
- getBox() - Method in class etomica.modules.droplet.MeterDeformation
-
- getBox() - Method in class etomica.modules.entropylottery.MeterEntropy
-
- getBox() - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- getBox() - Method in class etomica.modules.materialfracture.MeterElongation
-
- getBox() - Method in class etomica.modules.materialfracture.MeterStrain
-
- getBox() - Method in class etomica.modules.materialfracture.MeterStress
-
- getBox() - Method in class etomica.modules.materialfracture.StrainColorScheme
-
- getBox() - Method in class etomica.modules.multiharmonic.MeterFreeEnergy
-
- getBox() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- getBox() - Method in class etomica.modules.rosmosis.MeterFlux
-
- getBox() - Method in class etomica.modules.vle.MeterPressure2
-
- getBox() - Method in class etomica.molecule.MoleculeAgentManager
-
Convenience method to return the box the Manager is tracking.
- getBox() - Method in class etomica.normalmode.CoordinateDefinition
-
- getBox() - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
- getBox() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- getBox() - Method in class etomica.normalmode.MeterAPIPotentialEnergy
-
- getBox() - Method in class etomica.normalmode.MeterAtomicDisplacement
-
- getBox() - Method in class etomica.normalmode.MeterHarmonicEnergy
-
- getBox() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- getBox() - Method in class etomica.normalmode.MeterNormalMode
-
- getBox() - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- getBox() - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- getBox() - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- getBox() - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- getBox() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- getBox() - Method in class etomica.parser.ParmedStructure
-
Gets the (single, rectangular) box found in this Structure.
- getBox(int) - Method in class etomica.simulation.Simulation
-
Returns one of the simulation Boxes.
- getBox() - Method in class etomica.simulation.SimulationBoxEvent
-
- getBox() - Method in class etomica.space.Boundary
-
- getBox() - Method in class etomica.spin.MeterSpin
-
- getBox() - Method in class etomica.virial.MCMoveClusterAtomQ
-
- getBox() - Method in class etomica.virial.MeterSamplingWeight
-
- getBox() - Method in class etomica.virial.MeterVirial
-
- getBox() - Method in class etomica.virial.MeterVirialBD
-
- getBox() - Method in class etomica.virial.MeterVirialBDBin
-
- getBox() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- getBox() - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- getBox() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- getBox() - Method in class etomica.virial.MeterVirialExternalField
-
- getBox() - Method in class etomica.virial.MeterVirialExternalFieldConfined
-
- getBox() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined
-
- getBox() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
-
- getBox() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
-
- getBox() - Method in class etomica.virial.MeterVirialExternalFieldOverlapRho
-
- getBox() - Method in class etomica.virial.MeterVirialExternalFieldRho
-
- getBox() - Method in class etomica.virial.MeterVirialExternalFieldSW
-
- getBox() - Method in class etomica.virial.MeterVirialIC
-
- getBox() - Method in class etomica.virial.MeterVirialSWWE
-
- getBoxBoundaries() - Method in class etomica.server.representations.ConfigurationUpdate
-
- getBoxCount() - Method in class etomica.simulation.Simulation
-
- getBoxes() - Method in class etomica.simulation.Simulation
-
Get all boxes in the simulation.
- getBoxFactory() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- getBoxIndex() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- getBoxSize() - Method in class etomica.space.Boundary
-
Returns the length of the sides of a rectangular box oriented in the lab
frame and in which the boundary is inscribed.
- getBoxSize() - Method in class etomica.space.BoundaryDeformablePeriodic
-
Returns the length of the sides of a rectangular box oriented in the lab
frame and in which the boundary is inscribed.
- getBoxSize() - Method in class etomica.space.BoundaryRectangular
-
Returns a vector with elements equal to the lengths of the edges of
the boundary.
- getBoxSize() - Method in class etomica.space3d.BoundaryTruncatedOctahedron
-
- getButton() - Method in class etomica.graphics.DeviceButton
-
- getBXX() - Method in class etomica.models.rowley.P2RepRowley
-
- getBXXDimension() - Method in class etomica.models.rowley.P2RepRowley
-
- getByte1() - Method in class etomica.graph.engine.impl.BinaryOpByteImpl
-
- getByte1() - Method in class etomica.graph.engine.impl.UnaryOpByteImpl
-
- getByte1() - Method in class etomica.graph.engine.impl.UnaryOpTwoByteImpl
-
- getByte1() - Method in interface etomica.graph.engine.Parser.BinaryOpByte
-
- getByte1() - Method in interface etomica.graph.engine.Parser.UnaryOpByte
-
- getByte1() - Method in interface etomica.graph.engine.Parser.UnaryOpTwoByte
-
- getByte2() - Method in class etomica.graph.engine.impl.UnaryOpTwoByteImpl
-
- getByte2() - Method in interface etomica.graph.engine.Parser.UnaryOpTwoByte
-
- getC() - Method in class etomica.math.geometry.Plane
-
- getC() - Method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- getC() - Method in class etomica.modules.pistoncylinder.PistonPlane
-
- getC() - Method in class etomica.modules.sam.WallPlane
-
- getC() - Method in class etomica.potential.P2Exp6
-
- getC(int) - Method in class etomica.virial.cluster.ClusterOperations
-
- getC_2Type() - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- getC_3Type() - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- getCallCount() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- getCallCount() - Method in class etomica.normalmode.MeterNormalMode
-
- getCancelMap() - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- getCancelMap() - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- getCancelMap() - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- getCancelMap() - Method in class etomica.virial.cluster.VirialDiagrams
-
- getCancelMap() - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- getCancelMap() - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- getCancelMap() - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- getCancelMap() - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- getCanonicalCopy(float) - Method in class org.jmol.util.BoxInfo
-
- getCanonicalCopy(Point3f[], float) - Static method in class org.jmol.util.BoxInfo
-
- getCapSlabObject(String, boolean) - Static method in class org.jmol.util.MeshSurface
-
legacy -- for some scripts with early isosurface slabbing
- getCarbonType() - Method in class etomica.models.rowley.SpeciesEthanol
-
- getCarbonType() - Method in class etomica.virial.SpeciesTraPPECO2
-
- getCDimension() - Method in class etomica.potential.P2Exp6
-
- getCDimension() - Method in class etomica.potential.P2Exp6Buckingham
-
- getCell(IMolecule) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- getCell(IAtom) - Method in class etomica.nbr.cell.NeighborCellManager
-
- getCellAgentManager() - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- getCellAgentManager() - Method in class etomica.nbr.PotentialMasterNbr
-
- getCellRange() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Returns the cellRange.
- getCellRange() - Method in class etomica.nbr.cell.NeighborCellManager
-
Returns the cellRange.
- getCellRange() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- getCellRange() - Method in class etomica.nbr.list.PotentialMasterList
-
- getCellRange() - Method in class etomica.nbr.PotentialMasterHybrid
-
- getCellRange() - Method in class etomica.nbr.site.PotentialMasterSite
-
- getCellSize() - Method in class etomica.lattice.CellLattice
-
Returns the spatial dimensions of all cells in the lattice, such that a cell in the
lattice will have a size in each direction as given by the corresponding value
in the returned array.
- getCellSizeX() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- getCellSizeX() - Method in class etomica.modules.sam.ConfigurationSAM
-
- getCellSizeZ() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- getCellSizeZ() - Method in class etomica.modules.sam.ConfigurationSAM
-
- getCenter() - Method in class etomica.space.Boundary
-
- getCenterAndPoints(List<Point3f>) - Static method in class org.jmol.util.Measure
-
- getCenterOfRotation() - Method in class g3dsys.control.G3DSys
-
- getCH2element() - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- getCH2Type() - Method in class etomica.modules.sam.SpeciesAlkaneThiol
-
- getCH2Type() - Method in class etomica.virial.SpeciesAlkane
-
- getCH3element() - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- getCH3Type() - Method in class etomica.models.OPLS.SpeciesAceticAcid
-
- getCH3Type() - Method in class etomica.models.traPPE.SpeciesMethanol
-
- getCH3Type() - Method in class etomica.modules.sam.SpeciesAlkaneThiol
-
- getCH3Type() - Method in class etomica.virial.SpeciesAlkane
-
- getChainlength() - Method in class etomica.models.hexane.MCMoveCBMC
-
- getChainLength() - Method in class etomica.modules.colloid.ColloidSim
-
- getChainLength() - Method in class etomica.modules.colloid.ConfigurationColloid
-
- getChainLength() - Method in class etomica.modules.rheology.SimulationRheology
-
- getChainPhi(int) - Method in class etomica.modules.sam.Sam
-
- getChainPsi() - Method in class etomica.modules.sam.Sam
-
- getChainTheta() - Method in class etomica.modules.sam.Sam
-
- getChangeableColix(short, int) - Method in class org.jmol.util.GData
-
- getChangeableColixIndex(short) - Static method in class org.jmol.util.Colix
-
- getCharge(int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getCharge(int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getCharge(int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getCharge1() - Method in class etomica.potential.P2Electrostatic
-
Returns the charge on the first type of atom.
- getCharge1() - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
Returns the charge on the first type of atom.
- getCharge2() - Method in class etomica.potential.P2Electrostatic
-
Returns the charge on the second type of atom.
- getCharge2() - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
Returns the charge on the second type of atom.
- getChargeH() - Method in class etomica.models.water.P2Water4PSoft
-
- getChargeH() - Method in class etomica.models.water.P2WaterTIP4P
-
- getChargeM() - Method in class etomica.models.water.P2Water4PSoft
-
- getChargeM() - Method in class etomica.models.water.P2WaterTIP4P
-
- getCheckBox() - Method in class etomica.graphics.DeviceCheckBox
-
- getChi(double) - Method in class etomica.association.MCMoveAtomDimer
-
- getChi(double) - Method in class etomica.association.MCMoveAtomMonomer
-
- getChi(double) - Method in class etomica.association.MCMoveAtomNoSmer
-
- getChi(double) - Method in class etomica.association.MCMoveAtomSmer
-
- getChi(double) - Method in class etomica.association.MCMoveBiasUB
-
- getChi(double) - Method in class etomica.association.MCMoveBiasUBMolecule
-
- getChi(double) - Method in class etomica.association.MCMoveDimer
-
- getChi(double) - Method in class etomica.association.MCMoveDimerRotate
-
- getChi(double) - Method in class etomica.association.MCMoveMoleculeMonomer
-
- getChi(double) - Method in class etomica.association.MCMoveMoleculeRotateAssociated
-
- getChi(double) - Method in class etomica.association.MCMoveRotateAssociated
-
- getChi(double) - Method in class etomica.association.MCMoveRotateNoSmer
-
- getChi(double) - Method in class etomica.association.MCMoveSmer
-
- getChi(double) - Method in class etomica.association.MCMoveSmerRotate
-
- getChi(double) - Method in class etomica.association.MCMoveVolumeAssociated
-
- getChi(double) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- getChi(double) - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- getChi(double) - Method in class etomica.freeenergy.npath.MCMoveAtomNPath
-
- getChi(double) - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- getChi(double) - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMove
-
Chi is the parameter within standard Metropolis Monte Carlo.
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveAtom
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveBoxSize
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveDimer
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
-
- getChi(double) - Method in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- getChi(double) - Method in class etomica.models.hexane.MCMoveCBMC
-
- getChi(double) - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- getChi(double) - Method in class etomica.models.hexane.MCMoveReptate
-
- getChi(double) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- getChi(double) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- getChi(double) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- getChi(double) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- getChi(double) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- getChi(double) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- getChi(double) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- getChi(double) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- getChi(double) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- getChi(double) - Method in class etomica.modules.adsorption.MyMCMove
-
- getChi(double) - Method in class etomica.modules.dcvgcmd.MyMCMove
-
- getChi(double) - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- getChi(double) - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- getChi(double) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- getChi(double) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- getChi(double) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- getChi(double) - Method in class etomica.normalmode.MCMoveAtomSuperBox
-
- getChi(double) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- getChi(double) - Method in class etomica.normalmode.MCMoveHarmonic
-
- getChi(double) - Method in class etomica.normalmode.MCMoveHarmonicStep
-
- getChi(double) - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
- getChi(double) - Method in class etomica.normalmode.MCMovePhaseAngle
-
- getChi(double) - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- getChi(double) - Method in class etomica.normalmode.MCMoveSingleMode
-
- getChi(double) - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- getChi(double) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- getChi(double) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- getChi(double) - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- getChi(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- getChi(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- getChi(double) - Method in class etomica.normalmode.MCMoveWV
-
- getChi(double) - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- getChi(double) - Method in class etomica.spin.MCMoveSpinFlip
-
- getChi(double) - Method in class etomica.virial.MCMoveChangeBondLength
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterAngleBend
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- getChi() - Method in class etomica.virial.MCMoveClusterAtom
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterAtomDiscrete
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterAtomHSChain
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterAtomHSTree
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterAtomMulti
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterAtomQ
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterDiagram
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterMolecule
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterMoleculeMulti
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterPolyhedraChain
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterPolyhedraTree
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterRingRegrow
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterRingScale
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterRotateCH3
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- getChi(double) - Method in class etomica.virial.MCMoveClusterWiggleMulti
-
- getChi(double) - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
-
- getChildCount() - Method in class etomica.species.SpeciesSpheresHetero
-
Returns the number of child atoms of each type created by this factory.
- getChildList() - Method in interface etomica.molecule.IMolecule
-
Returns the atoms in the molecule as an IAtomList.
- getChildList() - Method in class etomica.molecule.Molecule
-
- getChildProperties() - Method in class etomica.meta.wrappers.Wrapper
-
- getCHType() - Method in class etomica.virial.SpeciesAnthracene3site464
-
- getCHType() - Method in class etomica.virial.SpeciesAnthracene3site545
-
- getCHType() - Method in class etomica.virial.SpeciesPh3site464
-
- getCHType() - Method in class etomica.virial.SpeciesPh3site545
-
- getCHType() - Method in class etomica.virial.SpeciesTraPPEAnthracene
-
- getCHType() - Method in class etomica.virial.SpeciesTraPPENaphthalene
-
- getCHType() - Method in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- getClasses() - Method in class etomica.meta.SimulationModel
-
- getCliqueCount() - Method in class etomica.virial.ClusterSumHS
-
- getCliqueCount() - Method in interface etomica.virial.ClusterWheatley
-
Returns number of cliques for the configuration passed to
checkConfig
- getCliqueCount() - Method in class etomica.virial.ClusterWheatleyHS
-
- getCliqueCount() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- getCliques() - Method in class etomica.virial.ClusterSumHS
-
- getCliques() - Method in interface etomica.virial.ClusterWheatley
-
Returns an array containing the clique sets for the configuration passed
to checkConfig.
- getCliques() - Method in class etomica.virial.ClusterWheatleyHS
-
- getCliques() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- getCloseWindow() - Method in class etomica.virial.GUI.views.ViewAlertMsgBox
-
- getCloseWindow() - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- getCloseWindow() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- getCluster() - Method in class etomica.modules.clustergenerator.ClusterPanel
-
- getCluster() - Method in class etomica.virial.MeterVirialExternalField
-
- getCluster() - Method in class etomica.virial.MeterVirialExternalFieldConfined
-
- getCluster() - Method in class etomica.virial.MeterVirialExternalFieldSW
-
- getClusters() - Method in class etomica.virial.ClusterSum
-
- getClusters() - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- getClusters() - Method in class etomica.virial.ClusterSumPolarizable
-
- getClusters() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- getClusters() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- getClusters() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- getClusters() - Method in class etomica.virial.ClusterWeightUmbrella
-
- getClusters() - Method in class etomica.virial.MeterVirial
-
- getClusters() - Method in class etomica.virial.MeterVirialBD
-
- getClusters() - Method in class etomica.virial.MeterVirialSWWE
-
- getCoeffAc(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOS
-
- getCoeffAc(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- getCoefficients() - Method in interface etomica.normalmode.WaveVectorFactory
-
Returns the coefficients for the wave vectors returned by
getWaveVectors.
- getCoefficients() - Method in class etomica.normalmode.WaveVectorFactory1D
-
- getCoefficients() - Method in class etomica.normalmode.WaveVectorFactory2D
-
- getCoefficients() - Method in class etomica.normalmode.WaveVectorFactoryFcc
-
- getCoefficients() - Method in class etomica.normalmode.WaveVectorFactoryFromFile
-
- getCoefficients() - Method in class etomica.normalmode.WaveVectorFactorySimple
-
- getColix(Color) - Static method in class g3dsys.control.G3DSys
-
Converts the given AWT color to a G3D Colix
- getColix(int) - Static method in class g3dsys.control.G3DSys
-
Converts the given argb int to a G3D Colix
- getColix(int) - Static method in class org.jmol.util.Colix
-
- getColixArray(String) - Static method in class org.jmol.util.Colix
-
- getColixInherited(short, short) - Static method in class org.jmol.util.Colix
-
- getColixO(Object) - Static method in class org.jmol.util.Colix
-
- getColixS(String) - Static method in class org.jmol.util.Colix
-
- getColixTranslucencyFractional(short) - Static method in class org.jmol.util.Colix
-
- getColixTranslucencyLevel(short) - Static method in class org.jmol.util.Colix
-
- getColixTranslucent(int) - Static method in class org.jmol.util.Colix
-
- getColixTranslucent3(short, boolean, float) - Static method in class org.jmol.util.Colix
-
- getCollisionCount() - Method in class etomica.integrator.IntegratorHard
-
- getCollisionDiameter() - Method in class etomica.potential.P2HardSphere
-
Accessor method for collision diameter
- getCollisionDiameterDimension() - Method in class etomica.potential.P2HardSphere
-
- getCollisionRadius() - Method in class etomica.modules.osmosis.MeterOsmoticPressure
-
Returns the collision radius used to calculate the accessible "area".
- getCollisionRadius() - Method in class etomica.modules.osmosis.P1HardWall
-
Distance from the center of the sphere to the boundary at collision.
- getCollisionRadius() - Method in class etomica.potential.P1HardBoundary
-
Distance from the center of the sphere to the boundary at collision.
- getCollisionRadius() - Method in class etomica.potential.P1HardMovingBoundary
-
Distance from the center of the sphere to the boundary at collision.
- getCollisionRadiusDimension() - Method in class etomica.modules.osmosis.P1HardWall
-
Indicates collision radius has dimensions of Length.
- getCollisionRadiusDimension() - Method in class etomica.potential.P1HardBoundary
-
Indicates collision radius has dimensions of Length.
- getCollisionRadiusDimension() - Method in class etomica.potential.P1HardMovingBoundary
-
Indicates collision radius has dimensions of Length.
- getColloidSigma() - Method in class etomica.modules.colloid.ColloidSim
-
- getColor() - Method in interface etomica.graph.model.Edge
-
- getColor() - Method in class etomica.graph.model.impl.EdgeImpl
-
- getColor() - Method in class etomica.graph.model.impl.MetadataImpl
-
- getColor() - Method in class etomica.graph.model.impl.NodeImpl
-
- getColor() - Method in interface etomica.graph.model.Metadata
-
- getColor() - Method in interface etomica.graph.model.Node
-
- getColor(AtomType) - Method in class etomica.graphics.ColorSchemeByType
-
- getColor() - Method in class g3dsys.images.Axes
-
- getColor() - Method in class g3dsys.images.Ball
-
- getColor() - Method in class g3dsys.images.Box
-
- getColor() - Method in class g3dsys.images.Ellipse
-
- getColor() - Method in class g3dsys.images.Line
-
- getColor() - Method in class g3dsys.images.Triangle
-
- getColor1() - Method in class etomica.graph.engine.impl.UnaryOpColorImpl
-
- getColor1() - Method in class etomica.graph.engine.impl.UnaryOpThreeColorImpl
-
- getColor1() - Method in interface etomica.graph.engine.Parser.UnaryOpColor
-
- getColor1() - Method in interface etomica.graph.engine.Parser.UnaryOpThreeColor
-
- getColor1() - Method in class g3dsys.images.Bond
-
- getColor2() - Method in class etomica.graph.engine.impl.UnaryOpThreeColorImpl
-
- getColor2() - Method in interface etomica.graph.engine.Parser.UnaryOpThreeColor
-
- getColor2() - Method in class g3dsys.images.Bond
-
- getColor3() - Method in class etomica.graph.engine.impl.UnaryOpThreeColorImpl
-
- getColor3() - Method in interface etomica.graph.engine.Parser.UnaryOpThreeColor
-
- getColorArgbOrGray(short) - Method in class org.jmol.util.GData
-
- getColorIn() - Method in class etomica.modules.crystalviewer.ColorSchemePlane
-
- getColorMap() - Method in class etomica.graph.engine.impl.UnaryOpByteMapImpl
-
- getColorMap() - Method in interface etomica.graph.engine.Parser.UnaryOpByteMap
-
- getColorOut() - Method in class etomica.modules.crystalviewer.ColorSchemePlane
-
- getColorScheme() - Method in class etomica.graphics.DisplayBox
-
Accessor method for the color scheme used for this display
- getColumn(int, float[]) - Method in class org.jmol.util.Matrix3f
-
Copies the matrix values in the specified column into the array parameter.
- getColumn(int, float[]) - Method in class org.jmol.util.Matrix4f
-
Copies the matrix values in the specified column into the array parameter.
- getColumnClass(int) - Method in class etomica.graphics.DeviceTableModelGeneric
-
- getColumnCount() - Method in class etomica.graphics.DeviceTableModelGeneric
-
Get the number of columns in the table
- getColumnCount() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- getColumnCount() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- getColumnCount() - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- getColumnInfoFactories() - Method in class etomica.data.types.DataTable.DataInfoTableFactory
-
Returns a copy of the array of DataInfoFactories for the columns
- getColumnName(int) - Method in class etomica.graphics.DeviceTableModelGeneric
-
- getColumnV(int, Vector3f) - Method in class org.jmol.util.Matrix3f
-
Copies the matrix values in the specified column into the vector parameter.
- getCombinationProbability() - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
Returns the probability that two radicals will bond instead of becoming
unreactive.
- getCommand() - Method in class etomica.graph.engine.impl.CommandImpl
-
- getCommand() - Method in interface etomica.graph.engine.Parser.Command
-
- getCommandSet(String) - Static method in class org.jmol.script.Token
-
retrieves an unsorted list of viable commands that could be
completed by this initial set of characters.
- getCompletedActions() - Method in interface etomica.action.activity.ActivityGroup
-
Returns all actions from this group that have been completed.
- getCompletedActions() - Method in class etomica.action.activity.ActivityGroupParallel
-
- getCompletedActions() - Method in class etomica.action.activity.ActivityGroupSeries
-
- getComponent() - Method in class etomica.graphics.DeviceSlider
-
- getComponent() - Method in class etomica.graphics.DeviceSpinner
-
- getComponents(Graph) - Static method in class etomica.graph.traversal.CVisitor
-
Returns the biconnected components of the given graph.
- getComponentSet() - Method in class etomica.meta.ComponentIndex
-
- getComponentValues() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getCOMType() - Method in class etomica.models.water.SpeciesWater4PCOM
-
- getConfigDLPOLY() - Method in class etomica.potential.PotentialDLPOLY
-
- getConfigP2DLPOLY() - Method in class etomica.potential.P2DLPOLY
-
- getConfiguration() - Method in class etomica.action.SimulationRestart
-
- getConfName() - Method in class etomica.action.WriteConfiguration
-
Returns the configuration name.
- getConfName() - Method in class etomica.action.WriteConfigurationBinary
-
Returns the configuration name.
- getConfName() - Method in class etomica.action.WriteConfigurationDLPOLY
-
Returns the configuration name.
- getConfName() - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
Returns the configuration name.
- getConformation() - Method in class etomica.chem.models.ModelChain
-
Returns the Conformation for the molecule, or null if no Conformation
has been set (a ConformationLinear will be used).
- getConformation(int) - Method in class etomica.modules.sam.ConfigurationSAM
-
- getConformation() - Method in class etomica.species.Species
-
- getConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getConsole() - Method in interface etomica.graph.engine.ConsoleContainer
-
- getConsole() - Method in class etomica.graph.engine.Launcher.ConsoleWindow
-
- getConstrainScriptOrigin() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Returns whether scripts can only be loaded from the same
origin as the documents referencing them.
- getConstraint() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- getConstraintAngle() - Method in class etomica.models.nitrogen.MeterDirectInitPert
-
- getConstructionInfo(Class, SimulationModel) - Static method in class etomica.server.core.construction.Construction
-
- getConstructorObject() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getContainingCubeEdgeLength() - Method in class etomica.math.geometry.TruncatedOctahedron
-
Returns the length of an edge of a cube in which the truncated octahedron
is inscribed.
- getController() - Method in class etomica.action.activity.ControllerEvent
-
- getController() - Method in interface etomica.action.ControllerAction
-
- getController() - Method in class etomica.action.ControllerActionAdapter
-
- getController() - Method in class etomica.graphics.Device
-
- getController() - Method in class etomica.graphics.DeviceControllerButton
-
- getController() - Method in class etomica.graphics.SimulationGraphic
-
- getController() - Method in class etomica.normalmode.SimOverlapModule
-
- getController() - Method in class etomica.simulation.Simulation
-
- getControllerButton() - Method in class etomica.graphics.DeviceTrioControllerButton
-
- getConvergence(Potential2SoftSpherical, int, double, double, boolean, boolean) - Static method in class etomica.virial.B3ForSphericallySymmetricU
-
- getConvergence(Potential2SoftSpherical, int, int, double, double, boolean) - Static method in class etomica.virial.BnIETP2Spherical
-
- getConvergence(Potential2SoftSpherical, int, int, double, double, boolean) - Static method in class etomica.virial.BnPY_1QC_Helium
-
- getConvergence(Potential2Spherical, int, double, double, double, boolean, double) - Static method in class etomica.virial.BnPYCHe
-
- getCoordinateDefinition() - Method in class etomica.conjugategradient.DerivativeEnergyFunction
-
- getCoordinateDefinition() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- getCoordinateDefinition() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- getCoordinateDefinition() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- getCoordinateDefinition() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- getCoordinateDefinition() - Method in class etomica.normalmode.IntegratorHarmonic
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MCMoveHarmonic
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MCMoveHarmonicStep
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MCMoveSingleMode
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MeterDDP
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MeterDP
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MeterHarmonicCoordinate
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MeterHarmonicEnergy
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MeterNormalMode
-
- getCoordinateDefinition() - Method in class etomica.normalmode.MeterTargetTP
-
- getCoordinateDefinition() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- getCoordinateDefinition() - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
-
- getCoordinateDefinitionParacetamol() - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
- getCoordinateDim() - Method in class etomica.normalmode.CoordinateDefinition
-
Returns the number of generalized coordinates associated with each
molecule.
- getCoordinates() - Method in class etomica.server.representations.ConfigurationUpdate
-
- getCoreDiameter() - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Accessor method for core diameter.
- getCoreDiameter() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Accessor method for core diameter.
- getCoreDiameter() - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Accessor method for core diameter.
- getCoreDiameter() - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Accessor method for core diameter.
- getCoreDiameter() - Method in class etomica.potential.P2DoubleWell
-
Accessor method for core diameter.
- getCoreDiameter() - Method in class etomica.potential.P2PenetrableSphere
-
Accessor method for core diameter.
- getCoreDiameter() - Method in class etomica.potential.P2PenetrableSquareWell
-
Accessor method for core diameter.
- getCoreDiameter() - Method in class etomica.potential.P2SquareWell
-
Accessor method for core diameter.
- getCoreDiameter() - Method in class etomica.potential.P2SquareWellRobust
-
Accessor method for core diameter.
- getCoreDiameter() - Method in class etomica.potential.P2TriangleWell
-
- getCoreDiameterDimension() - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- getCoreDiameterDimension() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- getCoreDiameterDimension() - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
- getCoreDiameterDimension() - Method in class etomica.modules.mu.P2SquareWellOneSide
-
- getCoreDiameterDimension() - Method in class etomica.potential.P2DoubleWell
-
- getCoreDiameterDimension() - Method in class etomica.potential.P2PenetrableSphere
-
- getCoreDiameterDimension() - Method in class etomica.potential.P2PenetrableSquareWell
-
- getCoreDiameterDimension() - Method in class etomica.potential.P2SquareWell
-
- getCoreDiameterDimension() - Method in class etomica.potential.P2SquareWellRobust
-
- getCoreDiameterDimension() - Method in class etomica.potential.P2TriangleWell
-
- getCoreEdgeCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getCoreIterator() - Method in class etomica.lattice.IndexIteratorTriangularPermutations
-
- getCoreLen() - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getCoreLen() - Method in interface etomica.graph.isomorphism.SearchState
-
- getCoreSet() - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getCoreSet() - Method in interface etomica.graph.isomorphism.SearchState
-
- getCount() - Method in class etomica.box.BoxMoleculeCountEvent
-
- getCount() - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getCount() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getCount() - Method in interface etomica.data.histogram.Histogram
-
Returns the number of times the Histogram's addValue method was called.
- getCount() - Method in class etomica.data.histogram.HistogramDiscrete
-
- getCount() - Method in class etomica.data.histogram.HistogramNotSoSimple
-
- getCount() - Method in class etomica.data.histogram.HistogramReweightedData
-
- getCount() - Method in class etomica.data.histogram.HistogramSimple
-
- getCount() - Method in class etomica.normalmode.HSNPT.ActionSummer
-
- getCountOfMoleculesStrings() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getCountOfSpeciesSLM(int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getCountOfSpeciesSLMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getCountSpecies(int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- getCoupling() - Method in class etomica.spin.P2Spin
-
- getCov(int, int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyDataCov
-
- getCPairID() - Method in class etomica.virial.BoxCluster
-
- getCPairID() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- getCPairSet() - Method in class etomica.virial.BoxCluster
-
returns the current coordinate pair set
- getCriteria() - Method in class etomica.potential.PotentialArray
-
- getCriteria() - Method in class etomica.potential.PotentialArrayMolecular
-
- getCriterion(ISpecies) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- getCriterion(IPotentialMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Returns the criterion used by to determine what atoms interact with the
given potential.
- getCriterion(AtomType) - Method in class etomica.nbr.list.NeighborListManager
-
- getCriterion(IPotentialAtomic) - Method in class etomica.nbr.list.PotentialMasterList
-
Returns the criterion used by to determine what atoms interact with the
given potential.
- getCriterion(IPotentialAtomic) - Method in class etomica.nbr.site.PotentialMasterSite
-
Returns the criterion used by to determine what atoms interact with the
given potential.
- getCriterion() - Method in class etomica.potential.Potential0
-
- getCriticalPoints(Point3f[], Tuple3f) - Static method in class org.jmol.util.BoxInfo
-
- getCType() - Method in class etomica.AlkaneEH.SpeciesMethane
-
- getCType() - Method in class etomica.models.OPLS.SpeciesAceticAcid
-
- getCType() - Method in class etomica.paracetamol.SpeciesParacetamol
-
- getCType() - Method in class etomica.virial.SpeciesAnthracene3site464
-
- getCType() - Method in class etomica.virial.SpeciesAnthracene3site545
-
- getCType() - Method in class etomica.virial.SpeciesMethane
-
- getCType() - Method in class etomica.virial.SpeciesPh3site464
-
- getCType() - Method in class etomica.virial.SpeciesPh3site545
-
- getCType() - Method in class etomica.virial.SpeciesTraPPEAnthracene
-
- getCType() - Method in class etomica.virial.SpeciesTraPPENaphthalene
-
- getCType() - Method in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- getCubicSize() - Method in class etomica.lattice.crystal.PrimitiveBcc
-
Returns the common length of all primitive vectors.
- getCubicSize() - Method in class etomica.lattice.crystal.PrimitiveFcc
-
Returns the common length of all primitive vectors.
- getCurrentActions() - Method in interface etomica.action.activity.ActivityGroup
-
Returns all actions from this group that are currently being performed.
- getCurrentActions() - Method in class etomica.action.activity.ActivityGroupParallel
-
- getCurrentActions() - Method in class etomica.action.activity.ActivityGroupSeries
-
- getCurrentLattice() - Method in class etomica.modules.crystalviewer.LatticeEditor
-
Returns the currently selected crystal.
- getCurrentStep() - Method in class etomica.action.ActionIntegrate
-
- getCurrentStep() - Method in class etomica.action.activity.ActivityIntegrate
-
- getCurrentTime() - Method in class etomica.integrator.IntegratorMD
-
- getCurrentTime() - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- getCurrentTime() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- getCutoff() - Method in class etomica.modules.droplet.AtomFilterLiquid
-
- getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- getCutoffFactorLJ() - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationCone
-
- getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSites
-
- getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
- getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationConeOneSite
-
- getCutoffFactorLJDimension() - Static method in class etomica.potential.P2HardAssociationConeSW
-
- getCXX() - Method in class etomica.models.rowley.P2RepRowley
-
- getD() - Method in class etomica.eigenstuff.MyEigenvalueDecomposition
-
Return the block diagonal eigenvalue matrix
- getD() - Method in interface etomica.lattice.IndexIterator
-
- getD() - Method in class etomica.lattice.IndexIteratorRectangular
-
Returns the length of the integer array that is returned as an iterate.
- getD() - Method in class etomica.lattice.IndexIteratorReflecting
-
- getD() - Method in class etomica.lattice.IndexIteratorTriangular
-
Returns the length of the int array that is returned as each iterate.
- getD() - Method in class etomica.lattice.IndexIteratorTriangularPermutations
-
- getD() - Method in class etomica.math.discrete.CombinationIterator
-
- getD() - Method in class etomica.math.discrete.PermutationDegenerateIterator
-
- getD() - Method in class etomica.math.discrete.PermutationIterator
-
- getD() - Method in class etomica.math.geometry.Plane
-
- getD() - Method in class etomica.modules.pistoncylinder.PistonPlane
-
- getD() - Method in class etomica.modules.sam.WallPlane
-
- getD(double, double, int) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- getD(double, double, int) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- getD(double, double, double) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- getD() - Method in class etomica.space.Space
-
- getD() - Method in interface etomica.space.Vector
-
Dimension of the space occupied by the vector.
- getD() - Method in class etomica.space1d.Vector1D
-
- getD() - Method in class etomica.space2d.Vector2D
-
- getD() - Method in class etomica.space3d.Vector3D
-
- getD() - Method in class etomica.spaceNd.VectorND
-
- getD() - Method in interface g3dsys.control.IndexIterator
-
Get the number of dimensions
- getD() - Method in class g3dsys.images.Axes
-
- getD() - Method in class g3dsys.images.Ball
-
- getD() - Method in class g3dsys.images.Bond
-
- getD() - Method in class g3dsys.images.Box
-
- getD() - Method in class g3dsys.images.Ellipse
-
- getD() - Method in class g3dsys.images.ImageShell
-
- getD() - Method in class g3dsys.images.Line
-
- getD2dfac() - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- getD2fac() - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- getD2Sum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- getD3dfac() - Method in class etomica.math.numerical.AkimaSplineSmoother
-
sets weight given to minimizing discontinuities in the 3nd derivative
(at data points)
- getD3fac() - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- getDADBSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
Returns sum of Fi dot ri
- getDADBSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
Returns sum of Fi dot ri
- getDADBXYZ() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- getData(AccumulatorAverage.StatType) - Method in class etomica.data.AccumulatorAverage
-
Returns a specific element from the DataGroup returned
by getData().
- getData() - Method in class etomica.data.AccumulatorAverageBlockless
-
Returns a DataGroup with Data instances holding the statistics kept by
this accumulator (as described in general comments for this class).
- getData() - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
Returns a DataGroup with Data instances holding the statistics kept by
this accumulator (as described in general comments for this class).
- getData() - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getData() - Method in class etomica.data.AccumulatorAverageCollapsing
-
- getData() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getData() - Method in class etomica.data.AccumulatorAverageCovariance
-
- getData() - Method in class etomica.data.AccumulatorAverageFixed
-
- getData() - Method in class etomica.data.AccumulatorAverageFixedOutputFile
-
Returns a DataGroup with Data instances holding the statistics kept by
this accumulator (as described in general comments for this class).
- getData() - Method in class etomica.data.AccumulatorCounter
-
Returns the DataInteger with the count.
- getData() - Method in class etomica.data.AccumulatorHistogram
-
Returns the set of histograms.
- getData() - Method in class etomica.data.AccumulatorHistory
-
Returns the set of histories.
- getData() - Method in class etomica.data.AccumulatorRatioAverageCovariance
-
- getData() - Method in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- getData() - Method in class etomica.data.DataAccumulator
-
- getData() - Method in class etomica.data.DataDump
-
- getData() - Method in class etomica.data.DataSet.DataSetSink
-
- getData(int) - Method in class etomica.data.DataSet
-
Returns the ith Data from the set.
- getData(IAtom) - Method in interface etomica.data.DataSourceAtomic
-
- getData() - Method in class etomica.data.DataSourceFunction
-
Returns the DataFunction made by this source.
- getData() - Method in class etomica.data.DataSourceGroup
-
Returns a DataGroup that is formed from the Data objects returned by
the data sources in this instance.
- getData(IMolecule) - Method in interface etomica.data.DataSourceMolecular
-
- getData() - Method in class etomica.data.DataSourcePoints
-
- getData(Vector) - Method in interface etomica.data.DataSourcePositioned
-
- getData(Vector) - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
-
- getData() - Method in class etomica.data.DataSourceRmsVelocity
-
Returns the rms velocity of the atoms given by the iterator.
- getData(IAtom) - Method in class etomica.data.DataSourceRmsVelocity
-
- getData() - Method in class etomica.data.DataSourceScalar
-
- getData() - Method in class etomica.data.DataSourceTensorVirialHard
-
Current value of the meter, obtained by dividing sum of collision virial contributions by time elapsed since last call.
- getData() - Method in class etomica.data.DataSourceUniform
-
Returns the uniformly spaced values.
- getData() - Method in class etomica.data.HistogramDataSource
-
Returns the set of histograms.
- getData() - Method in interface etomica.data.IDataSource
-
- getData() - Method in class etomica.data.meter.MeterDihedralAngle
-
Returns the Dihedral distribution, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (# of bins).
- getData() - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- getData() - Method in class etomica.data.meter.MeterHyperVirial
-
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
- getData() - Method in class etomica.data.meter.MeterMomentumCOM
-
Returns the instantaneous total center-of-mass momentum over all atoms in the box.
- getData(IMolecule) - Method in class etomica.data.meter.MeterNMolecules
-
- getData() - Method in class etomica.data.meter.MeterPositionCOM
-
Returns the position of the center of mass of all atoms in the box.
- getData() - Method in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
-
- getData() - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
- getData() - Method in class etomica.data.meter.MeterPressureHardTensor
-
- getData() - Method in class etomica.data.meter.MeterPressureTensor
-
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
- getData() - Method in class etomica.data.meter.MeterPressureTensorFromIntegrator
-
- getData() - Method in class etomica.data.meter.MeterProfile
-
Returns the profile for the current configuration.
- getData() - Method in class etomica.data.meter.MeterProfileByAtoms
-
Returns the profile for the current configuration.
- getData() - Method in class etomica.data.meter.MeterProfileByVolume
-
Returns the profile for the current configuration.
- getData() - Method in class etomica.data.meter.MeterRDF
-
Returns the RDF, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (xMax or # of bins).
- getData() - Method in class etomica.data.meter.MeterRDFPC
-
Returns the RDF, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (xMax or # of bins).
- getData() - Method in class etomica.data.meter.MeterStructureFactor
-
- getData() - Method in class etomica.data.meter.MeterTensorVelocity
-
Returns the velocity dyad (mass*vv) summed over all atoms, and divided by N
- getData(IAtom) - Method in class etomica.data.meter.MeterTensorVelocity
-
Returns the velocity dyad (mass*vv) for the given atom.
- getData() - Method in class etomica.data.types.DataDoubleArray
-
Returns the encapsulated array.
- getData() - Method in class etomica.data.types.DataDoubleBDArray
-
Returns the encapsulated array.
- getData(int) - Method in class etomica.data.types.DataGroup
-
Returns the i-th data element in the group, counting from 0.
- getData() - Method in class etomica.freeenergy.npath.DataSourceEnergies
-
- getData() - Method in class etomica.gaussianwork.MeterBoltzmannA
-
- getData() - Method in class etomica.gaussianwork.MeterBoltzmannB
-
- getData() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- getData() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- getData() - Method in class etomica.integrator.IntegratorGear4NPH.MeterEnthalpy
-
- getData() - Method in class etomica.integrator.IntegratorPT.BoxTracker
-
Returns array y such that y[i] is the current
box of the configuration that began in box i.
- getData() - Method in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
Computes total potential energy for box.
- getData() - Method in class etomica.liquidLJ.MeterPU
-
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
- getData() - Method in class etomica.liquidLJ.MeterPUCut
-
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
- getData() - Method in class etomica.liquidLJ.MeterPUCutLS
-
- getData() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
Performs a Widom insertion average, doing nInsert insertion attempts
Temperature used to get exp(-uTest/kT) is that of the integrator for the
box
- getData() - Method in class etomica.mappedRdf.MeterMappedRdf
-
Returns the RDF, averaged over the calls to actionPerformed since the
meter was reset or had some parameter changed (xMax or # of bins).
- getData() - Method in class etomica.mappedvirial.MeterMeanForce
-
- getData() - Method in class etomica.metastable.MeterDensityDistribution
-
- getData() - Method in class etomica.models.nitrogen.MeterBoltzmann
-
- getData() - Method in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- getData() - Method in class etomica.models.nitrogen.MeterNormalizedCoord
-
Returns the DataGroup of uDistribtion[i]
- getData() - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta
-
Returns the DataGroup of uDistribtion[i]
- getData() - Method in class etomica.models.nitrogen.MeterOrientationDistribution
-
Returns the DataGroup of uDistribtion[i]
- getData() - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup
-
Returns the DataGroup of uDistribtion[i]
- getData() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- getData() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- getData() - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
-
- getData() - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
-
- getData() - Method in class etomica.models.oneDHardRods.MeterOverlap
-
- getData() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
- getData() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D
-
- getData() - Method in class etomica.modules.adsorption.DataSourceDensityFunction
-
- getData() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- getData() - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- getData() - Method in class etomica.modules.droplet.MeterDeformation
-
- getData() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- getData() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
-
- getData(IMolecule) - Method in class etomica.modules.interfacial.MeterOrientation
-
- getData() - Method in class etomica.modules.mu.DataSourceWallPressureMu
-
- getData() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- getData() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getData() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
Implements DataSource interface, but you probably want to
getData for a specific Bennet parameter.
- getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- getData() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- getData() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- getData() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getData() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getData() - Method in class etomica.modules.pistoncylinder.MeterRDFCylinder
-
- getData() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- getData() - Method in class etomica.modules.rosmosis.MeterFlux
-
- getData() - Method in class etomica.modules.rosmosis.MeterOsmoticPressure
-
- getData() - Method in class etomica.modules.sam.MeterTilt
-
- getData() - Method in class etomica.modules.statistics.DataCollector
-
- getData() - Method in class etomica.normalmode.DataSourceFE
-
- getData() - Method in class etomica.normalmode.DataSourceFEHistogram
-
- getData() - Method in class etomica.normalmode.DataSourceImposedFEFit
-
- getData() - Method in class etomica.normalmode.DataSourceImposedFEHistogram
-
- getData() - Method in class etomica.normalmode.DataSourcePMu
-
- getData() - Method in class etomica.normalmode.DataSourcePN
-
- getData() - Method in class etomica.normalmode.MeterAtomicDisplacement
-
- getData() - Method in class etomica.normalmode.MeterBoltzmann
-
- getData() - Method in class etomica.normalmode.MeterBoltzmannHarmonic
-
- getData() - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- getData() - Method in class etomica.normalmode.MeterBoltzmannTarget
-
Sets the fraction that the system is coupled to measured energy.
- getData() - Method in class etomica.normalmode.MeterDADB
-
- getData() - Method in class etomica.normalmode.MeterDDP
-
- getData() - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- getData() - Method in class etomica.normalmode.MeterDirectSamplingTarget
-
- getData() - Method in class etomica.normalmode.MeterDP
-
- getData() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- getData() - Method in class etomica.normalmode.MeterNormalMode
-
Returns the DataGroup of S(k) Tensors corresponding to the sum of
T(k)*transpose(T(-k)).
- getData() - Method in class etomica.normalmode.MeterOverlapSwitch
-
- getData() - Method in class etomica.normalmode.MeterPlaneSlip
-
- getData() - Method in class etomica.normalmode.MeterSamplingHarmonic
-
- getData() - Method in class etomica.normalmode.MeterSamplingTarget
-
- getData() - Method in class etomica.normalmode.MeterSolidDA
-
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
- getData() - Method in class etomica.normalmode.MeterSolidDACut
-
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
- getData() - Method in class etomica.normalmode.MeterSolidMirror
-
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
- getData() - Method in class etomica.normalmode.MeterSolidProps
-
- getData() - Method in class etomica.normalmode.MeterSolidPropsLJ
-
- getData() - Method in class etomica.normalmode.MeterTargetTP
-
- getData() - Method in class etomica.normalmode.MeterTilt
-
- getData() - Method in class etomica.normalmode.MeterTiltHistogram
-
- getData() - Method in class etomica.normalmode.MeterTiltRotation
-
- getData() - Method in class etomica.normalmode.MeterTiltRotationHistogram
-
- getData() - Method in class etomica.normalmode.MeterTiltRotationStdev
-
- getData() - Method in class etomica.normalmode.MeterWorkBennetHarmonic
-
- getData() - Method in class etomica.normalmode.MeterWorkBennetTarget
-
- getData() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- getData() - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- getData() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- getData() - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- getData() - Method in class etomica.normalmode.MeterWorkTargetBennet
-
- getData() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- getData() - Method in class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- getData() - Method in class etomica.normalmode.MeterWorkTargetUmbrella
-
- getData() - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- getData() - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- getData() - Method in class etomica.overlap.MeterOverlap
-
- getData() - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic.LatticeEnergy
-
- getData() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol.Lattice2ndDerivative
-
- getData() - Method in class etomica.potential.P2QChemInterpolated
-
- getData() - Method in class etomica.potential.P3HydrogenManzhos
-
- getData() - Method in class etomica.server.representations.DataAndInfo
-
- getData() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- getData() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- getData() - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- getData() - Method in class etomica.virial.MeterSamplingWeight
-
- getData() - Method in class etomica.virial.MeterVirial
-
- getData() - Method in class etomica.virial.MeterVirialBD
-
- getData() - Method in class etomica.virial.MeterVirialExternalField
-
- getData() - Method in class etomica.virial.MeterVirialExternalFieldConfined
-
- getData() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined
-
- getData() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
-
- getData() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
-
- getData() - Method in class etomica.virial.MeterVirialExternalFieldOverlapRho
-
- getData() - Method in class etomica.virial.MeterVirialExternalFieldRho
-
- getData() - Method in class etomica.virial.MeterVirialExternalFieldSW
-
- getData() - Method in class etomica.virial.MeterVirialIC
-
- getData() - Method in class etomica.virial.MeterVirialSWWE
-
- getData() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
Implements DataSource interface, but you probably want to
getData for a specific Bennet parameter.
- getData(int) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
Return all standard data corresponding to the given Bennet parameter.
- getDataAsArray() - Method in class etomica.data.meter.MeterMeanSquareDisplacement
-
- getDataAsScalar() - Method in class etomica.association.MeterDimerMoleFraction
-
- getDataAsScalar() - Method in class etomica.data.AccumulatorHistory.DataSourceCount
-
- getDataAsScalar() - Method in class etomica.data.DataSourceAcceptanceProbability
-
Returns the value of the acceptance ratios as currently kept by
the MCMove classes identified with setMove.
- getDataAsScalar() - Method in class etomica.data.DataSourceAcceptanceRatio
-
Returns the value of the acceptance ratio as currently kept by
the MCMove class identified with setMove.
- getDataAsScalar() - Method in class etomica.data.DataSourceAtomDistance
-
- getDataAsScalar() - Method in class etomica.data.DataSourceCountCollisions
-
Returns the simulation time elapsed by the integrator tracked
by this class since the last reset.
- getDataAsScalar() - Method in class etomica.data.DataSourceCountSteps
-
Returns the number of steps performed by the integrator
- getDataAsScalar() - Method in class etomica.data.DataSourceCountTime
-
Returns the simulation time elapsed by the integrator tracked
by this class since the last reset.
- getDataAsScalar() - Method in class etomica.data.DataSourceScalar
-
Returns a single scalar value as the measurement for the given box.
- getDataAsScalar() - Method in class etomica.data.meter.MeterAvgBondLength
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterDensity
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterDipoleSumSquared1site
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterDipoleSumSquaredTIP4PWater
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterEnergy
-
Current value of the total energy (kinetic + potential)
- getDataAsScalar() - Method in class etomica.data.meter.MeterKineticEnergy
-
Returns the total kinetic energy summed over all atoms produced by
the iterator when applied to the given box.
- getDataAsScalar() - Method in class etomica.data.meter.MeterKineticEnergyFromIntegrator
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterKineticEnergyRigid
-
Returns the total kinetic energy summed over all atoms produced by
the iterator when applied to the given box.
- getDataAsScalar() - Method in class etomica.data.meter.MeterLocalDensity
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterLocalMoleFraction
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterMeanSquareDisplacement
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterMoleFraction
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterNMolecules
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterPotentialEnergy
-
Computes total potential energy for box.
- getDataAsScalar() - Method in class etomica.data.meter.MeterPotentialEnergyFromIntegrator
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterPressure
-
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
- getDataAsScalar() - Method in class etomica.data.meter.MeterPressureHard
-
Returns P = (NT - (virial sum)/((elapsed time)*T*(space dimension)))/V
Virial sum and elapsed time apply to period since last call to this method.
- getDataAsScalar() - Method in class etomica.data.meter.MeterPressureMolecular
-
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
- getDataAsScalar() - Method in class etomica.data.meter.MeterRadiusGyration
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterRMSD
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterTemperature
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterVolume
-
- getDataAsScalar() - Method in class etomica.data.meter.MeterWidomInsertion
-
Performs a Widom insertion average, doing nInsert insertion attempts
Temperature used to get exp(-uTest/kT) is that of the integrator for the
box
- getDataAsScalar() - Method in class etomica.interfacial.MeterWallForce
-
- getDataAsScalar() - Method in class etomica.interfacial.MeterWallPosition
-
- getDataAsScalar() - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Performs a Widom insertion average, doing nInsert insertion attempts
Temperature used to get exp(-uTest/kT) is that of the integrator for the
box
- getDataAsScalar() - Method in class etomica.mappedvirial.MeterMappedU
-
- getDataAsScalar() - Method in class etomica.mappedvirial.MeterMappedVirial
-
- getDataAsScalar() - Method in class etomica.mappedvirial.MeterMappedVirialV
-
- getDataAsScalar() - Method in class etomica.models.nitrogen.MeterBoltzmannDirect
-
- getDataAsScalar() - Method in class etomica.models.nitrogen.MeterDirectInitPert
-
- getDataAsScalar() - Method in class etomica.models.nitrogen.MeterOrientationOrderParameter
-
- getDataAsScalar() - Method in class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAddDoubleSize
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterDifferentImageSubtractDoubleSize
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterF
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- getDataAsScalar() - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- getDataAsScalar() - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- getDataAsScalar() - Method in class etomica.modules.catalysis.MeterDensityCO
-
- getDataAsScalar() - Method in class etomica.modules.catalysis.MeterDensityCO2
-
- getDataAsScalar() - Method in class etomica.modules.catalysis.MeterDensityO2
-
- getDataAsScalar() - Method in class etomica.modules.chainequilibrium.MeterConversion
-
- getDataAsScalar() - Method in class etomica.modules.colloid.MeterEnd2End
-
- getDataAsScalar() - Method in class etomica.modules.dcvgcmd.MeterFlux
-
- getDataAsScalar() - Method in class etomica.modules.droplet.DropletAtomicGraphic.DataSourceVaporDensity
-
- getDataAsScalar() - Method in class etomica.modules.entropylottery.MeterEntropy
-
- getDataAsScalar() - Method in class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterElongation
-
- getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterLoad
-
- getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterStrain
-
- getDataAsScalar() - Method in class etomica.modules.materialfracture.MeterStress
-
- getDataAsScalar() - Method in class etomica.modules.mu.MeterDensitySides
-
- getDataAsScalar() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
-
- getDataAsScalar() - Method in class etomica.modules.multiharmonic.MeterFreeEnergy
-
- getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceChiSlope
-
- getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa
-
- getDataAsScalar() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
-
- getDataAsScalar() - Method in class etomica.modules.osmosis.MeterOsmoticPressure
-
- getDataAsScalar() - Method in class etomica.modules.pistoncylinder.DataSourceWallPressure
-
- getDataAsScalar() - Method in class etomica.modules.rheology.MeterEndToEnd
-
- getDataAsScalar() - Method in class etomica.modules.rheology.MeterNormalStress
-
- getDataAsScalar() - Method in class etomica.modules.rheology.MeterViscosity
-
- getDataAsScalar() - Method in class etomica.modules.sam.MeterWallPressure
-
- getDataAsScalar() - Method in class etomica.modules.vle.MeterPressure2
-
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceAvgPressure
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceAvgPressure2
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootDPressure
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootDU
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootPressure
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot.DataSourceMuRootVacancyConcentration
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootPressure
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot1.DataSourceMuRootVacancyConcentration
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRoot1
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootPressure
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRootPMatch.DataSourceMuRootVacancyConcentration
-
- getDataAsScalar() - Method in class etomica.normalmode.DataSourceMuRootPMatch
-
- getDataAsScalar() - Method in class etomica.normalmode.MeterAPIPotentialEnergy
-
- getDataAsScalar() - Method in class etomica.normalmode.MeterDisplacementMoleculeRMS
-
- getDataAsScalar() - Method in class etomica.normalmode.MeterDisplacementRMS
-
- getDataAsScalar() - Method in class etomica.normalmode.MeterHarmonicCoordinate
-
- getDataAsScalar() - Method in class etomica.normalmode.MeterHarmonicEnergy
-
- getDataAsScalar() - Method in class etomica.normalmode.MeterHarmonicEnergyFromMove
-
- getDataAsScalar() - Method in class etomica.normalmode.MeterJacobian
-
- getDataAsScalar() - Method in class etomica.normalmode.MeterMaxExpansion
-
- getDataAsScalar() - Method in class etomica.normalmode.MeterPhiDeviation
-
- getDataAsScalar() - Method in class etomica.normalmode.MeterPressureSuperBox
-
Computes total pressure in box by summing virial over all pairs, and adding
ideal-gas contribution.
- getDataAsScalar() - Method in class etomica.normalmode.MeterThetaDeviation
-
- getDataAsScalar() - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- getDataAsScalar() - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- getDataAsScalar() - Method in class etomica.normalmode.SimOverlapLJModule.MeterPotentialEnergyDifference
-
- getDataAsScalar() - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- getDataAsScalar() - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- getDataAsScalar() - Method in class etomica.spin.MeterSpin
-
- getDataCount() - Method in class etomica.data.DataSet
-
- getDataDouble() - Method in class etomica.data.DataSourceScalar
-
Causes the single getDataAsScalar(Box) value to be computed and
returned for the given box.
- getDataFromSet(DataTag[]) - Method in class etomica.graphics.DisplayPlot
-
- getDataHistogramBetaUAWf() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- getDataHistogramBetaUAWf() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- getDataHistogramBetaUAWr() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- getDataHistogramBetaUAWr() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- getDataHistogramBetaUBWf() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- getDataHistogramBetaUBWf() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- getDataHistogramBetaUBWr() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- getDataHistogramBetaUBWr() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- getDataImaginary(int, int) - Method in class etomica.lattice.LatticeSumCrystal.DataGroupLSC
-
Returns imaginary part of complex data.
- getDataImaginary(int, int) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular.DataGroupLSC
-
Returns imaginary part of complex data.
- getDataImaginary(int, int) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol.DataGroupLSCParacetamol
-
Returns imaginary part of complex data.
- getDataInfo() - Method in class etomica.data.AccumulatorHistogram
-
Returns the DataInfo for the output Data.
- getDataInfo() - Method in class etomica.data.AccumulatorHistory
-
- getDataInfo() - Method in class etomica.data.DataDump
-
- getDataInfo() - Method in class etomica.data.DataProcessor
-
- getDataInfo() - Method in class etomica.data.DataSet.DataSetSink
-
- getDataInfo(int) - Method in class etomica.data.DataSet
-
Returns the ith DataInfo from the set.
- getDataInfo() - Method in class etomica.data.DataSourceFunction
-
- getDataInfo() - Method in class etomica.data.DataSourceGroup
-
- getDataInfo() - Method in class etomica.data.DataSourcePoints
-
- getDataInfo() - Method in class etomica.data.DataSourceRmsVelocity
-
- getDataInfo() - Method in class etomica.data.DataSourceScalar
-
- getDataInfo() - Method in class etomica.data.DataSourceTensorVirialHard
-
- getDataInfo() - Method in class etomica.data.DataSourceUniform
-
- getDataInfo() - Method in interface etomica.data.FunctionData
-
Returns a DataInfo that describes the Data object that is returned by this function's f method.
- getDataInfo() - Method in class etomica.data.HistogramDataSource
-
Returns the DataInfo for the output Data.
- getDataInfo() - Method in interface etomica.data.IDataSource
-
- getDataInfo() - Method in class etomica.data.meter.MeterDihedralAngle
-
- getDataInfo() - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- getDataInfo() - Method in class etomica.data.meter.MeterHyperVirial
-
- getDataInfo() - Method in class etomica.data.meter.MeterMomentumCOM
-
- getDataInfo() - Method in class etomica.data.meter.MeterPositionCOM
-
- getDataInfo() - Method in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
-
- getDataInfo() - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
- getDataInfo() - Method in class etomica.data.meter.MeterPressureHardTensor
-
- getDataInfo() - Method in class etomica.data.meter.MeterPressureTensor
-
- getDataInfo() - Method in class etomica.data.meter.MeterPressureTensorFromIntegrator
-
- getDataInfo() - Method in class etomica.data.meter.MeterProfile
-
- getDataInfo() - Method in class etomica.data.meter.MeterProfileByAtoms
-
- getDataInfo() - Method in class etomica.data.meter.MeterProfileByVolume
-
- getDataInfo() - Method in class etomica.data.meter.MeterRDF
-
- getDataInfo() - Method in class etomica.data.meter.MeterRDFPC
-
- getDataInfo() - Method in class etomica.data.meter.MeterStructureFactor
-
- getDataInfo() - Method in class etomica.data.meter.MeterTensorVelocity
-
- getDataInfo() - Method in class etomica.freeenergy.npath.DataSourceEnergies
-
- getDataInfo() - Method in class etomica.gaussianwork.MeterBoltzmannA
-
- getDataInfo() - Method in class etomica.gaussianwork.MeterBoltzmannB
-
- getDataInfo() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- getDataInfo() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- getDataInfo() - Method in class etomica.integrator.IntegratorGear4NPH.MeterEnthalpy
-
- getDataInfo() - Method in class etomica.integrator.IntegratorPT.BoxTracker
-
- getDataInfo() - Method in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- getDataInfo() - Method in class etomica.liquidLJ.MeterPU
-
- getDataInfo() - Method in class etomica.liquidLJ.MeterPUCut
-
- getDataInfo() - Method in class etomica.liquidLJ.MeterPUCutLS
-
- getDataInfo() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- getDataInfo() - Method in class etomica.mappedRdf.MeterMappedRdf
-
- getDataInfo() - Method in class etomica.mappedvirial.MeterMeanForce
-
- getDataInfo() - Method in class etomica.metastable.MeterDensityDistribution
-
- getDataInfo() - Method in class etomica.models.nitrogen.MeterBoltzmann
-
- getDataInfo() - Method in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- getDataInfo() - Method in class etomica.models.nitrogen.MeterNormalizedCoord
-
- getDataInfo() - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta
-
- getDataInfo() - Method in class etomica.models.nitrogen.MeterOrientationDistribution
-
- getDataInfo() - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup
-
- getDataInfo() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- getDataInfo() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- getDataInfo() - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
-
- getDataInfo() - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
-
- getDataInfo() - Method in class etomica.models.oneDHardRods.MeterOverlap
-
- getDataInfo() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
- getDataInfo() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D
-
- getDataInfo() - Method in class etomica.modules.adsorption.DataSourceDensityFunction
-
- getDataInfo() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- getDataInfo() - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- getDataInfo() - Method in class etomica.modules.droplet.MeterDeformation
-
- getDataInfo() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- getDataInfo() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
-
- getDataInfo() - Method in class etomica.modules.mu.DataSourceWallPressureMu
-
- getDataInfo() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- getDataInfo() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- getDataInfo() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- getDataInfo() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- getDataInfo() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getDataInfo() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getDataInfo() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- getDataInfo() - Method in class etomica.modules.rosmosis.MeterFlux
-
- getDataInfo() - Method in class etomica.modules.rosmosis.MeterOsmoticPressure
-
- getDataInfo() - Method in class etomica.modules.sam.MeterTilt
-
- getDataInfo() - Method in class etomica.modules.statistics.DataCollector
-
- getDataInfo() - Method in class etomica.normalmode.DataSourceFE
-
- getDataInfo() - Method in class etomica.normalmode.DataSourceFEHistogram
-
- getDataInfo() - Method in class etomica.normalmode.DataSourceImposedFEFit
-
- getDataInfo() - Method in class etomica.normalmode.DataSourceImposedFEHistogram
-
- getDataInfo() - Method in class etomica.normalmode.DataSourcePMu
-
- getDataInfo() - Method in class etomica.normalmode.DataSourcePN
-
- getDataInfo() - Method in class etomica.normalmode.MeterAtomicDisplacement
-
- getDataInfo() - Method in class etomica.normalmode.MeterBoltzmann
-
- getDataInfo() - Method in class etomica.normalmode.MeterBoltzmannHarmonic
-
- getDataInfo() - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- getDataInfo() - Method in class etomica.normalmode.MeterBoltzmannTarget
-
- getDataInfo() - Method in class etomica.normalmode.MeterDADB
-
- getDataInfo() - Method in class etomica.normalmode.MeterDDP
-
- getDataInfo() - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- getDataInfo() - Method in class etomica.normalmode.MeterDirectSamplingTarget
-
- getDataInfo() - Method in class etomica.normalmode.MeterDP
-
- getDataInfo() - Method in class etomica.normalmode.MeterHarmonicCoordinate
-
- getDataInfo() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- getDataInfo() - Method in class etomica.normalmode.MeterNormalMode
-
- getDataInfo() - Method in class etomica.normalmode.MeterOverlapSwitch
-
- getDataInfo() - Method in class etomica.normalmode.MeterPlaneSlip
-
- getDataInfo() - Method in class etomica.normalmode.MeterSamplingHarmonic
-
- getDataInfo() - Method in class etomica.normalmode.MeterSamplingTarget
-
- getDataInfo() - Method in class etomica.normalmode.MeterSolidDA
-
- getDataInfo() - Method in class etomica.normalmode.MeterSolidDACut
-
- getDataInfo() - Method in class etomica.normalmode.MeterSolidMirror
-
- getDataInfo() - Method in class etomica.normalmode.MeterSolidProps
-
- getDataInfo() - Method in class etomica.normalmode.MeterSolidPropsLJ
-
- getDataInfo() - Method in class etomica.normalmode.MeterTargetTP
-
- getDataInfo() - Method in class etomica.normalmode.MeterTilt
-
- getDataInfo() - Method in class etomica.normalmode.MeterTiltHistogram
-
- getDataInfo() - Method in class etomica.normalmode.MeterTiltRotation
-
- getDataInfo() - Method in class etomica.normalmode.MeterTiltRotationHistogram
-
- getDataInfo() - Method in class etomica.normalmode.MeterTiltRotationStdev
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkBennetHarmonic
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkBennetTarget
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkTargetBennet
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkTargetUmbrella
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- getDataInfo() - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- getDataInfo() - Method in class etomica.overlap.MeterOverlap
-
- getDataInfo() - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic.LatticeEnergy
-
- getDataInfo() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol.Lattice2ndDerivative
-
- getDataInfo() - Method in class etomica.server.representations.DataAndInfo
-
- getDataInfo(String, String) - Method in class etomica.server.resources.data.DataStreamResource
-
- getDataInfo() - Method in class etomica.virial.MeterSamplingWeight
-
- getDataInfo() - Method in class etomica.virial.MeterVirial
-
- getDataInfo() - Method in class etomica.virial.MeterVirialBD
-
- getDataInfo() - Method in class etomica.virial.MeterVirialBDBin
-
- getDataInfo() - Method in class etomica.virial.MeterVirialExternalField
-
- getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldConfined
-
- getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined
-
- getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
-
- getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
-
- getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldOverlapRho
-
- getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldRho
-
- getDataInfo() - Method in class etomica.virial.MeterVirialExternalFieldSW
-
- getDataInfo() - Method in class etomica.virial.MeterVirialIC
-
- getDataInfo() - Method in class etomica.virial.MeterVirialSWWE
-
- getDataInfoHistogramBetaUAWf() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- getDataInfoHistogramBetaUAWf() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- getDataInfoHistogramBetaUAWr() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- getDataInfoHistogramBetaUAWr() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- getDataInfoHistogramBetaUBWf() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- getDataInfoHistogramBetaUBWf() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- getDataInfoHistogramBetaUBWr() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- getDataInfoHistogramBetaUBWr() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- getDataLength() - Method in class etomica.integrator.IntegratorPT.BoxTracker
-
- getDataOverlap() - Method in class etomica.normalmode.SimOverlapModule
-
- getDataPumps() - Method in class etomica.thermointegration.IntegratorThermodynamic
-
- getDataReal(int, int) - Method in class etomica.lattice.LatticeSumCrystal.DataGroupLSC
-
Returns real part of complex data.
- getDataReal(int, int) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular.DataGroupLSC
-
Returns real part of complex data.
- getDataReal(int, int) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol.DataGroupLSCParacetamol
-
Returns real part of complex data.
- getDataResetAction() - Method in class etomica.action.SimulationRestart
-
- getDataReweighted() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- getDataReweighted() - Method in class etomica.normalmode.MeterWorkTargetBennet
-
- getDataReweighted() - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- getDataReweighted() - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- getDataSet() - Method in class etomica.graphics.DisplayPlot
-
Returns the DataSinkTable instance that specifies the plot data.
- getDataSink(int) - Method in class etomica.data.DataDistributer
-
Returns the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
- getDataSink(int) - Method in class etomica.data.DataGroupSplitter
-
Returns the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
- getDataSink() - Method in class etomica.data.DataProcessor
-
- getDataSink() - Method in class etomica.data.DataProcessorForked
-
- getDataSink(int) - Method in class etomica.data.DataSplitter
-
Returns the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
- getDataSink(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
-
- getDataSink(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsingSplit
-
- getDataSinks() - Method in class etomica.data.DataFork
-
- getDataSinks() - Method in interface etomica.data.DataPipeForked
-
- getDataSinks() - Method in class etomica.data.DataProcessorForked
-
- getDataSource() - Method in class etomica.data.DataPump
-
- getDataSource() - Method in class etomica.data.meter.MeterProfile
-
The meter that defines the profiled quantity
- getDataSource() - Method in class etomica.data.meter.MeterProfileByAtoms
-
The meter that defines the profiled quantity
- getDataSource() - Method in class etomica.data.meter.MeterProfileByVolume
-
The meter that defines the profiled quantity
- getDataStreamPumps() - Method in class etomica.action.SimulationDataAction
-
- getDataStreamPumps() - Method in class etomica.graphics.DeviceTrioControllerButton
-
Returns an ArrayList of DataPumps that are headers for the data streams.
- getDataTable() - Method in class etomica.graphics.DisplayTable
-
- getDataTagBag(LinkedList<DataTagBag>, DataTag[]) - Static method in class etomica.graphics.DataTagBag
-
Returns the first DataTagBag from the given list that has no non-matching
tags with the given desiredTags
- getDataTagBagExact(LinkedList<DataTagBag>, DataTag[]) - Static method in class etomica.graphics.DataTagBag
-
Return the DataTagBag with the given set of tags (exactly) if it exists,
or null of no such DataTagBag exists.
- getDateFormat() - Method in interface org.jmol.api.ApiPlatform
-
- getDateFormat() - Method in class org.jmol.awt.Platform
-
- getDBOType() - Method in class etomica.models.OPLS.SpeciesAceticAcid
-
- getDecimalSliderMajorTickSpacing() - Method in class etomica.graphics.DecimalSlider
-
- getDecimalSliderMaximum() - Method in class etomica.graphics.DecimalSlider
-
- getDecimalSliderMinimum() - Method in class etomica.graphics.DecimalSlider
-
- getDecimalSliderMinorTickSpacing() - Method in class etomica.graphics.DecimalSlider
-
- getDecimalSliderValue() - Method in class etomica.graphics.DecimalSlider
-
- getDefaultColor() - Method in class etomica.graphics.ColorScheme
-
- getDefaultFontFamily() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getDeformation() - Method in class etomica.modules.droplet.ConfigurationDroplet
-
- getDegeneracy() - Method in class etomica.math.discrete.PermutationDegenerateIterator
-
- getDelayExponent() - Method in class etomica.graphics.DeviceDelaySlider
-
- getDeltaCut() - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- getDeltaCut() - Method in class etomica.virial.ClusterSumPolarizable
-
- getDeltaCut() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- getDeltaCut() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- getDeltaCut() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- getDeltaN() - Method in class etomica.modules.dcvgcmd.MyMCMove
-
- getDeltaU(IAtomKinetic, double, boolean, boolean) - Method in class etomica.modules.mu.P1MagicWall
-
- getDeltaU(double) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- getDeltaX() - Method in class etomica.data.histogram.HistogramExpanding
-
- getDenominator() - Method in interface etomica.graph.model.Coefficient
-
- getDenominator() - Method in class etomica.graph.model.impl.CoefficientImpl
-
- getDenstiyProfileDump() - Method in class etomica.data.DataProcessorChemicalPotential
-
- getDepth() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Get depth percentage
- getDepth() - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Get depth percentage
- getDepth() - Method in class org.jmol.util.GData
-
gets g3d depth
- getDepthPercent() - Method in class g3dsys.control.G3DSys
-
- getDescent() - Method in class org.jmol.util.JmolFont
-
- getDescription(String) - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getDescription(String) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getDescription() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getDescription() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getDestination() - Method in class etomica.action.MoleculeActionTranslateTo
-
- getDestinationFile(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Get the name of the result image file.
- getDestinationType() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getDeviationVector() - Method in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
-
- getdFdr(double) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- getdFdr(double) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- getdfdT(int, double, double) - Static method in class etomica.virial.B3LJ
-
Returns a discretized df/dT function containing N points with a
separation interval of del_r
- getDiameter(IAtom) - Method in interface etomica.atom.DiameterHash
-
Returns an appropriate diameter for the given atom.
- getDiameter(IAtom) - Method in class etomica.atom.DiameterHashByElement
-
- getDiameter(IElement) - Method in class etomica.atom.DiameterHashByElement
-
- getDiameter(IAtom) - Method in class etomica.atom.DiameterHashByElementType
-
- getDiameter(IAtom) - Method in class etomica.atom.DiameterHashByType
-
- getDiameter(AtomType) - Method in class etomica.atom.DiameterHashByType
-
- getDiameterHash() - Method in class etomica.graphics.DisplayBox
-
Returns the DiameterHash used by this DisplayBox.
- getDiameterHashByElement() - Method in class etomica.atom.DiameterHashByElementType
-
- getDielectric() - Method in class etomica.potential.P2ReactionFieldDipole
-
- getDielectric() - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
Returns the dielectric constant of the fluid surrounding the cavity.
- getDiffusePercent() - Static method in class org.jmol.util.GData
-
- getDim() - Method in class etomica.modules.rosmosis.MeterFlux
-
- getDimension() - Method in class etomica.conjugategradient.DerivativeEnergyFunction
-
- getDimension() - Method in class etomica.conjugategradient.TestFiniteDifferenceDerivative
-
- getDimension() - Method in class etomica.conjugategradient.TestNonLinearConjugateGradients
-
- getDimension() - Method in class etomica.data.DataInfo
-
- getDimension() - Method in class etomica.data.DataInfoFactory
-
Returns the dimension
- getDimension() - Method in interface etomica.data.IDataInfo
-
- getDimension() - Method in interface etomica.data.IDataInfoFactory
-
Returns the dimension
- getDimension() - Method in class etomica.data.meter.MeterTemperature
-
- getDimension() - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- getDimension() - Method in class etomica.graphics.Device
-
- getDimension() - Method in interface etomica.math.function.FunctionMultiDimensional
-
The dimension of the space of independent variables.
- getDimension() - Method in class etomica.math.numerical.CalcGradientDifferentiable
-
- getDimension() - Method in class etomica.math.numerical.FiniteDifferenceDerivative
-
- getDimension() - Method in interface etomica.modifier.Modifier
-
Returns the dimension of the property being modified.
- getDimension() - Method in class etomica.modifier.ModifierGeneral
-
- getDimension() - Method in class etomica.modifier.ModifierNMolecule
-
- getDimension() - Method in class etomica.modifier.ModifyAction
-
- getDimension() - Method in class etomica.modules.adsorption.ModifierPMu
-
- getDimension(double, double) - Method in class etomica.modules.clustergenerator.Plot
-
Computes the separation in pixels of two points in the world window.
- getDimension() - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
-
- getDimension() - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
-
- getDimension() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
-
- getDimension() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
-
- getDimension() - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- getDimension() - Method in class etomica.modules.entropylottery.ModifierDimensions
-
- getDimension() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- getDimension() - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- getDimension() - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- getDimension() - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- getDimension() - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
-
- getDimension() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
-
- getDimension() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
-
- getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
-
- getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
-
- getDimension() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- getDimension() - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
-
- getDimension() - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
-
- getDimension() - Method in class etomica.normalmode.ModifierCells3D
-
- getDimension() - Method in class etomica.normalmode.ModifierXCells2D
-
- getDimension() - Method in class etomica.normalmode.ModifierYCells2D
-
- getDimension() - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
-
- getDimension() - Method in class etomica.virial.simulations.ModifierTPI
-
- getDimensions() - Method in class etomica.lattice.CellLattice
-
Returns the array that specifies the spatial dimensions of the lattice of cells.
- getDimerAtomType() - Method in class etomica.normalmode.SpeciesHSDimer
-
- getDimx() - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- getDimy() - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- getDipole(IMolecule) - Method in class etomica.AlkaneEH.DHS_NVT.DipoleSourceDHS
-
- getDipole(IMolecule) - Method in class etomica.AlkaneEH.DLJ_NVT_1site.DipoleSourceDLJ
-
- getDipole(IMolecule) - Method in class etomica.dielectric.DHS_NVT.DipoleSourceDHS
-
- getDipole(IMolecule) - Method in class etomica.dielectric.DLJ_NVT_1site.DipoleSourceDLJ
-
- getDipole(IMolecule) - Method in class etomica.dielectric.TIP4P_NVT.DipoleSourceTIP4PWater
-
- getDipole(IMolecule) - Method in class etomica.models.OPLS.DipoleSourceAceticAcid
-
- getDipole(IMolecule) - Method in class etomica.models.water.DipoleSourceWater
-
- getDipole(IMolecule) - Method in interface etomica.molecule.DipoleSource
-
Returns the dipole of the given molecule.
- getDipole1() - Method in class etomica.models.water.P2WaterTIP4PHardCore
-
- getDipole1() - Method in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
-
- getDipole2() - Method in class etomica.models.water.P2WaterTIP4PHardCore
-
- getDipole2() - Method in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
-
- getDipoleMomentSquare() - Method in class etomica.rotation.P2LJDipole
-
- getDipoleSource() - Method in class etomica.potential.P2ReactionFieldDipole
-
The DipoleSource returns the dipole vector of a given molecule.
- getDipoleSource() - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
Returns the dipole source used by this object.
- getDipoleStrength() - Method in class etomica.models.water.DipoleSourceWater
-
Returns the dipole strength.
- getDirectedNormalThroughPoints(Point3f, Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- getDirection() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Gets the direction (up or down list) of the neighbors given by the iterator.
- getDirection() - Method in interface etomica.space.IOrientation
-
- getDirection() - Method in class etomica.space1d.Orientation1D
-
- getDirection() - Method in class etomica.space2d.Orientation2D
-
- getDirection() - Method in class etomica.space3d.Orientation3D
-
- getDirection() - Method in class etomica.space3d.OrientationFull3D
-
- getDirection() - Method in class etomica.spin.P1MagneticField
-
- getDiscardProperty() - Method in class etomica.graph.operations.SplitParameters
-
- getDisplacement(IAtom) - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- getDisplayBox(Box) - Method in class etomica.graphics.SimulationGraphic
-
- getDisplayDensity() - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- getDisplayDensity() - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- getDisplayDensity() - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- getDisplayPlot() - Method in class etomica.graphics.DevicePlotPoints
-
Returns the top level panel that the function plot components sit on.
- getDistanceToOrigin() - Method in class etomica.math.geometry.Plane
-
Perpendicular distance from the plane to the origin.
- getDitheredNoisyShadeIndex(float, float, float, float) - Static method in class org.jmol.util.Shader
-
- getDoApplyPBC() - Method in class etomica.action.WriteConfiguration
-
Returns true if PBC are applied to coordinates written to the file.
- getDoApplyPBC() - Method in class etomica.action.WriteConfigurationBinary
-
Returns true if PBC are applied to coordinates written to the file.
- getDoApplyPBC() - Method in class etomica.action.WriteConfigurationDLPOLY
-
Returns true if PBC are applied to coordinates written to the file.
- getDoApplyPBC() - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
Returns true if PBC are applied to coordinates written to the file.
- getDoApplyPBC() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- getDoApplyPBC() - Method in class etomica.nbr.cell.NeighborCellManager
-
- getDoApplyPBC() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- getDoApplyPBC() - Method in class etomica.nbr.list.NeighborListManager
-
- getDoAveraging() - Method in class etomica.data.histogram.HistogramNotSoSimple
-
- getDoCov() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- getDoEnforceBounds() - Method in class etomica.data.DataSourceUniform
-
- getDoExcludeNonNeighbors() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
Returns true if the move does not explicitly calculate the potential for
atom pairs that are not neighbors (as determined by the potentialMaster).
- getDoExcludeNonNeighbors() - Method in class etomica.normalmode.MCMoveAtomCoupled
-
Returns true if the move does not explicitly calculate the potential for
atom pairs that are not neighbors (as determined by the potentialMaster).
- getDoExcludeNonNeighbors() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
Returns true if the move does not explicitly calculate the potential for
atom pairs that are not neighbors (as determined by the potentialMaster).
- getDoPrevious() - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- getDoShowCurrent() - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- getDoStrictBlockData() - Method in class etomica.data.AccumulatorAverageFixed
-
- getDoubleArray() - Method in class etomica.math.Quaternion
-
Returns the Quaternion as a double array
- getDoubleAvg() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- getDoubleDefaultParameters(String) - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getDoubleDefaultParameters(String) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getDoubleVar() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- getDoWiggle() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- getDownList() - Method in class etomica.nbr.list.AtomNeighborLists
-
Returns an array of downlist-neighbor-atom lists.
- getDownList() - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists
-
Returns an array of downlist-neighbor-molecule lists.
- getDownList(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- getDownList(IAtom) - Method in class etomica.nbr.list.NeighborListManager
-
- getDrawables() - Method in class etomica.graphics.DisplayBox
-
- getDrawBoundary() - Method in class etomica.graphics.DisplayCanvas
-
- getDrawBoundaryType() - Method in class g3dsys.images.ImageShell
-
Gets the boundary drawing style
- getDrawingHeight() - Method in class etomica.graphics.DisplayBox
-
return int : height of the drawing area (only relevant for 1D)
- getDrawOverflow() - Method in class etomica.graphics.DisplayBox
-
- getDrawSize() - Method in class etomica.graphics.DisplayBox
-
- getDrawSize() - Method in class etomica.graphics.DisplayPolytope
-
- getDst() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getDUDW(IAtomList) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- getDump() - Method in class etomica.server.dao.DataStreamStore.DataPlumbing
-
- getDv() - Method in class etomica.modules.droplet.P2Cohesion
-
- getDy12(int) - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- getE1() - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getE1(byte, byte) - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getE2() - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getE2(byte, byte) - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getE2CliqueCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getE2Cliques() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getECliqueCount() - Method in class etomica.virial.ClusterSumHS
-
- getECliqueCount() - Method in interface etomica.virial.ClusterWheatley
-
Returns number of e-bond cliques for the configuration passed to
checkConfig
- getECliqueCount() - Method in class etomica.virial.ClusterWheatleyHS
-
- getECliqueCount() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- getECliques() - Method in class etomica.virial.ClusterSumHS
-
- getECliques() - Method in interface etomica.virial.ClusterWheatley
-
Returns an array containing the clique sets (based on e-bonds) for the
configuration passed to checkConfig.
- getECliques() - Method in class etomica.virial.ClusterWheatleyHS
-
- getECliques() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- getEdge(byte) - Method in interface etomica.graph.model.Graph
-
- getEdge(byte, byte) - Method in interface etomica.graph.model.Graph
-
- getEdge(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- getEdge(byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- getEdgeCount() - Method in class etomica.virial.ClusterSumHS
-
Returns edgeCount (number of overlaps) of configuration passed to
checkConfig
- getEdgeCount() - Method in interface etomica.virial.ClusterWheatley
-
Returns edgeCount (number of overlaps) of configuration passed to
checkConfig
- getEdgeCount() - Method in class etomica.virial.ClusterWheatleyHS
-
Returns edgeCount (number of overlaps) of configuration passed to
checkConfig
- getEdgeCount() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
Returns edgeCount (number of overlaps) of configuration passed to
checkConfig
- getEdgeId(byte, byte) - Method in interface etomica.graph.model.Graph
-
- getEdgeId(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- getEdgeLength() - Method in class etomica.math.geometry.Cube
-
- getEdgeLength() - Method in class etomica.math.geometry.Square
-
- getEdgeLength() - Method in class etomica.math.geometry.TruncatedOctahedron
-
- getEdgeLengths() - Method in class etomica.math.geometry.Cuboid
-
Returns a vector with elements equal to the
edge lengths of the cuboid.
- getEdgeLengths() - Method in class etomica.math.geometry.LineSegment
-
Returns the length of the line segment as the element of a 1D vector.
- getEdgeLengths() - Method in class etomica.math.geometry.Rectangle
-
Returns a vector with elements equal to the
edge lengths of the rectangle.
- getEdgeLengths() - Method in interface etomica.math.geometry.Rectangular
-
- getEdges() - Method in class etomica.math.geometry.LineSegment
-
- getEdges() - Method in class etomica.math.geometry.Point
-
- getEdges() - Method in class etomica.math.geometry.Polygon
-
Returns all edges defined by the polygon.
- getEdges() - Method in class etomica.math.geometry.Polyhedron
-
Returns all edges defined by the polyhedron.
- getEdges() - Method in class etomica.math.geometry.Polytope
-
- getEdgeVector(int) - Method in class etomica.space.Boundary
-
Returns the vector that defines the edge of this boundary for the given
dimension.
- getEdgeVector(int) - Method in class etomica.space.BoundaryDeformablePeriodic
-
- getEdgeVector(int) - Method in class etomica.space.BoundaryRectangular
-
- getEdgeVector(int) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
-
- getEditValues() - Method in class etomica.graphics.DeviceSlider
-
- getEditVariables() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getEditVariables() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getEFCliqueCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getEFCliques() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getEigenvalues() - Method in class org.jmol.util.Eigen
-
- getEigenvectors() - Method in interface etomica.normalmode.NormalModes
-
First index corresponds to the wave vector; second index gives the eigenvector, and
third index gives the elements of the vector.
- getEigenvectors() - Method in class etomica.normalmode.NormalModes1DHR
-
- getEigenvectors() - Method in class etomica.normalmode.NormalModes2D
-
- getEigenvectors() - Method in class etomica.normalmode.NormalModes3D
-
- getEigenvectors() - Method in class etomica.normalmode.NormalModesFromFile
-
- getEigenvectors() - Method in class etomica.normalmode.NormalModesMolecular
-
- getEigenvectors() - Method in class etomica.normalmode.NormalModesPotential
-
- getEigenvectors() - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- getEigenVectors() - Method in class etomica.normalmode.NormalModesVariable
-
- getEigenvectors() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- getEigenVectors3() - Method in class org.jmol.util.Eigen
-
- getEigenvectorsFloatTransposed() - Method in class org.jmol.util.Eigen
-
transpose V and turn into floats
- getElectrostatic() - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- getElement() - Method in class etomica.atom.AtomType
-
- getElement() - Method in class etomica.chem.models.ModelChain
-
Returns the Element used for the leaf atoms in the chain, or null if no
Element has been set (an ElementSimple will be used).
- getElement(int, int) - Method in class org.jmol.util.Matrix3f
-
Retrieves the value at the specified row and column of this matrix.
- getElement(int, int) - Method in class org.jmol.util.Matrix4f
-
Retrieves the value at the specified row and column of this matrix.
- getElementHash() - Method in class etomica.action.WriteConfigurationDLPOLY
-
- getElementHash() - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
- getElementNumber(short) - Static method in class org.jmol.util.Elements
-
- getEligibleConstructor(Class) - Static method in class etomica.server.core.construction.Construction
-
- getEllipsoid(Vector3f[], float[], boolean) - Static method in class org.jmol.util.Eigen
-
- getEllipsoidDD(double[][]) - Static method in class org.jmol.util.Eigen
-
- getEllipsoidShade(float, float, float, int, Matrix4f) - Static method in class org.jmol.util.Shader
-
- getEmbeddedSpace() - Method in class etomica.math.geometry.Polytope
-
The space defining the vectors used to represent the vertices.
- getEnabled() - Method in class etomica.util.Grabber.DefaultMouseListener
-
- getEnd() - Method in class g3dsys.images.Line
-
- getEndpoint1() - Method in class g3dsys.images.Bond
-
- getEndpoint2() - Method in class g3dsys.images.Bond
-
- getEnergy() - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- getEnergy(double[]) - Method in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- getEnergy(double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- getEnergy(double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- getEnergy(double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- getEnergy(double[]) - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- getEnergy(Vector[], Vector[]) - Method in class etomica.potential.P2WaterPotentialsJankowski
-
- getEnergySum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- getEnergySum() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- getEntries() - Method in class etomica.virial.ClusterWheatleyPartitionScreening.FrequencyCounter
-
- getEpsilon() - Method in class etomica.models.water.P2Water3P
-
- getEpsilon() - Method in class etomica.models.water.P2Water3PSoft
-
- getEpsilon() - Method in class etomica.models.water.P2Water4P
-
- getEpsilon() - Method in class etomica.models.water.P2Water4PSoft
-
- getEpsilon() - Method in class etomica.models.water.P2WaterTIP4P
-
- getEpsilon() - Method in class etomica.models.water.P2WaterTIP4PHardCore
-
- getEpsilon() - Method in class etomica.modules.adsorption.P1Wall
-
- getEpsilon() - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Accessor method for depth of well
- getEpsilon() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Accessor method for depth of well
- getEpsilon() - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Accessor method for depth of well
- getEpsilon() - Method in class etomica.modules.colloid.P1Wall
-
- getEpsilon() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- getEpsilon() - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
- getEpsilon() - Method in class etomica.modules.droplet.P2Cohesion
-
- getEpsilon() - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Accessor method for depth of well
- getEpsilon() - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
-
- getEpsilon() - Method in class etomica.modules.rosmosis.P1Tether
-
- getEpsilon() - Method in class etomica.modules.sam.P1WCAWall
-
- getEpsilon() - Method in class etomica.modules.vle.VLESim
-
- getEpsilon() - Method in class etomica.potential.P22CLJQ
-
- getEpsilon() - Method in class etomica.potential.P2Exp6Buckingham
-
- getEpsilon() - Method in class etomica.potential.P2HardAssociation
-
Accessor method for depth of well.
- getEpsilon() - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for Lennard-Jones energy parameter
- getEpsilon() - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for Lennard-Jones energy parameter
- getEpsilon() - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for Lennard-Jones energy parameter
- getEpsilon() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for Lennard-Jones energy parameter
- getEpsilon() - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for Lennard-Jones energy parameter
- getEpsilon() - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for Lennard-Jones energy parameter
- getEpsilon() - Method in class etomica.potential.P2LennardJones
-
Accessor method for Lennard-Jones energy parameter
- getEpsilon() - Method in class etomica.potential.P2LennardJonesDreiding
-
Accessor method for Lennard-Jones energy parameter
- getEpsilon() - Method in class etomica.potential.P2LJDipole
-
- getEpsilon() - Method in class etomica.potential.P2LJQ
-
- getEpsilon() - Method in class etomica.potential.P2LJQQ
-
- getEpsilon() - Method in class etomica.potential.P2ModifiedMorse
-
- getEpsilon() - Method in class etomica.potential.P2Morse
-
- getEpsilon() - Method in class etomica.potential.P2PenetrableSphere
-
Mutator method for height of core.
- getEpsilon() - Method in class etomica.potential.P2PenetrableSquareWell
-
Accessor method for depth of well
- getEpsilon() - Method in class etomica.potential.P2SoftSphere
-
Accessor method for soft-sphere energy parameter
- getEpsilon() - Method in class etomica.potential.P2SquareWell
-
Accessor method for depth of well
- getEpsilon() - Method in class etomica.potential.P2SquareWellRobust
-
Accessor method for depth of well
- getEpsilon() - Method in class etomica.potential.P2TriangleWell
-
- getEpsilon() - Method in class etomica.potential.P2WCA
-
Accessor method for the energy parameter
- getEpsilon() - Method in class etomica.potential.P3BondAngle
-
Returns the characteristic energy of the potential
- getEpsilon() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
Returns the characteristic energy of the potential
- getEpsilon() - Method in class etomica.rotation.P2LJDipole
-
- getEpsilon() - Method in class etomica.units.systems.LJ
-
- getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getEpsilon(int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getEpsilon() - Method in class etomica.yukawa.P2HC2Yukawa
-
- getEpsilon6() - Method in class etomica.potential.P2Exp6Buckingham
-
- getEpsilonBonding() - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- getEpsilonBonding() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- getEpsilonC() - Method in class etomica.potential.P2CO2EMP
-
- getEpsilonCG() - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- getEpsilonCO() - Method in class etomica.potential.P2CO2EMP
-
- getEpsilonCore() - Method in class etomica.potential.P2DoubleWell
-
Accessor method for depth of well
- getEpsilonCore() - Method in class etomica.potential.P2PenetrableSquareWell
-
- getEpsilonCoreDimension() - Method in class etomica.potential.P2PenetrableSquareWell
-
- getEpsilonDimension() - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- getEpsilonDimension() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- getEpsilonDimension() - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
- getEpsilonDimension() - Method in class etomica.modules.mu.P2SquareWellOneSide
-
- getEpsilonDimension() - Method in class etomica.potential.P2DoubleWell
-
- getEpsilonDimension() - Method in class etomica.potential.P2HardAssociation
-
- getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationCone
-
- getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSites
-
- getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
- getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeOneSite
-
- getEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeSW
-
- getEpsilonDimension() - Method in class etomica.potential.P2LennardJones
-
- getEpsilonDimension() - Method in class etomica.potential.P2LennardJonesDreiding
-
- getEpsilonDimension() - Method in class etomica.potential.P2ModifiedMorse
-
- getEpsilonDimension() - Method in class etomica.potential.P2Morse
-
- getEpsilonDimension() - Method in class etomica.potential.P2PenetrableSphere
-
- getEpsilonDimension() - Method in class etomica.potential.P2PenetrableSquareWell
-
- getEpsilonDimension() - Method in class etomica.potential.P2SoftSphere
-
- getEpsilonDimension() - Method in class etomica.potential.P2SquareWell
-
- getEpsilonDimension() - Method in class etomica.potential.P2SquareWellRobust
-
- getEpsilonDimension() - Method in class etomica.potential.P2TriangleWell
-
- getEpsilonDimension() - Method in class etomica.potential.P2WCA
-
- getEpsilonDimension() - Method in class etomica.potential.P3BondAngle
-
- getEpsilonDimension() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- getEpsilonNR() - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- getEpsilonO() - Method in class etomica.potential.P2CO2EMP
-
- getEpsilonWell() - Method in class etomica.potential.P2DoubleWell
-
- getEpsInner() - Method in class etomica.potential.P2PenetrableBond
-
- getEpsInnerDimension() - Method in class etomica.potential.P2PenetrableBond
-
- getEpsOuter() - Method in class etomica.potential.P2PenetrableBond
-
- getEpsOuterDimension() - Method in class etomica.potential.P2PenetrableBond
-
- getEquationForQuadricWithCenter(float, float, float, Matrix3f, Vector3f, Matrix3f, double[], Matrix4f) - Static method in class org.jmol.util.Quadric
-
- getError(int) - Method in interface etomica.overlap.DataOverlap.DataSourceOverlapAvg
-
- getError(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
-
- getError(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgSimple
-
- getError(int) - Method in class etomica.overlap.DataOverlap
-
Returns the error in the ratio of the reference to target
overlap-to-virial ratios (which reduces to target/reference)
for the given value of the Bennet parameter.
- getError() - Method in class etomica.virial.overlap.DataSourceVirialOverlap
-
Returns the error in the ratio of the reference to target
overlap-to-virial ratios (which reduces to target/reference)
for the optimal value of the Bennet parameter.
- getError(int) - Method in class etomica.virial.overlap.DataSourceVirialOverlap
-
Returns the error in the ratio of the reference to target
overlap-to-virial ratios (which reduces to target/reference)
for the given value of the Bennet parameter.
- getErrorCode() - Method in exception etomica.graph.view.rasterizer.SVGConverterException
-
- getEta(int) - Method in class etomica.virial.cluster.ClusterOperations
-
Returns all diagrams of order n in the expansion for the indirect correlation function eta(r) = h(r) - c(r),
in the presence of any approximations currently in effect.
- getEValNum() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
- getEValNum() - Method in class etomica.normalmode.IntegratorHarmonic
-
- getEventInterval() - Method in class etomica.integrator.Integrator
-
- getEventManager() - Method in class etomica.action.activity.Controller
-
Returns the event manager used by the controller to notify listeners of
individual actions events as well as events related to the controller
itself.
- getEventManager() - Method in class etomica.box.Box
-
- getEventManager() - Method in class etomica.integrator.Integrator
-
- getEventManager() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- getEventManager() - Method in class etomica.nbr.list.NeighborListManager
-
- getEventManager() - Method in class etomica.simulation.Simulation
-
- getEventManager() - Method in class etomica.space.Boundary
-
- getException(IAction) - Method in class etomica.action.activity.Controller
-
Returns the exception thrown by an action held by the controller.
- getExecuteOnload() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Returns true if the scripts attached to the DOM using 'onload'
event attribute is going to be executed before rasterizing,
false otherwise.
- getExp() - Method in class etomica.virial.MayerSSSeries
-
Returns the HS diameter.
- getExpGroupingSize() - Method in class etomica.util.ScientificFormat
-
- getExpMaximumIntegerDigits() - Method in class etomica.util.ScientificFormat
-
- getExpMinimumIntegerDigits() - Method in class etomica.util.ScientificFormat
-
- getExpNegativePrefix() - Method in class etomica.util.ScientificFormat
-
- getExpNegativeSuffix() - Method in class etomica.util.ScientificFormat
-
- getExponent() - Method in class etomica.potential.P2SoftSphere
-
Accessor method for soft-sphere softness parameter
- getExportName() - Method in class org.jmol.g3d.Graphics3D
-
- getExportType() - Method in class org.jmol.g3d.Graphics3D
-
- getExpPositivePrefix() - Method in class etomica.util.ScientificFormat
-
- getExpPositiveSuffix() - Method in class etomica.util.ScientificFormat
-
- getExpression() - Method in class etomica.graph.engine.impl.AssignmentImpl
-
- getExpression() - Method in class etomica.graph.engine.impl.UnaryOpImpl
-
- getExpression() - Method in interface etomica.graph.engine.Parser.Assignment
-
- getExpression() - Method in interface etomica.graph.engine.Parser.UnaryOp
-
- getExpression1() - Method in class etomica.graph.engine.impl.BinaryOpImpl
-
- getExpression1() - Method in interface etomica.graph.engine.Parser.BinaryOp
-
- getExpression2() - Method in class etomica.graph.engine.impl.BinaryOpImpl
-
- getExpression2() - Method in interface etomica.graph.engine.Parser.BinaryOp
-
- getExtension() - Method in class etomica.graph.view.rasterizer.DestinationType
-
- getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.VirialDiagrams
-
- getExtraDisconnectedVirialGraphs(int[]) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- getExtraDisconnectedVirialGraphs(int) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- getExtraDisconnectedVirialGraphs() - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- getExtrapolatedLogError(int, int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
-
- getExtraTargetClusters() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- getF(double) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- getF(double) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- getF1CliqueCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getF1Cliques() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getFaces() - Method in class etomica.math.geometry.Polyhedron
-
Returns all faces defined by the polyhedron.
- getFaces() - Method in class org.jmol.util.MeshSurface
-
- getFacesFromCriticalPoints(Point3f[]) - Static method in class org.jmol.util.BoxInfo
-
- getFaceVertexes(int) - Static method in class org.jmol.util.Geodesic
-
- getFactory() - Method in interface etomica.data.IDataInfo
-
Returns a mutable factory that can make copies of this instance of
DataInfo.
- getFactory() - Method in class etomica.data.types.DataDouble.DataInfoDouble
-
- getFactory() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
-
- getFactory() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
-
- getFactory() - Method in class etomica.data.types.DataFunction.DataInfoFunction
-
- getFactory() - Method in class etomica.data.types.DataGroup.DataInfoGroup
-
- getFactory() - Method in class etomica.data.types.DataTable.DataInfoTable
-
- getFactory() - Method in class etomica.data.types.DataTensor.DataInfoTensor
-
- getFactory() - Method in class etomica.data.types.DataVector.DataInfoVector
-
- getFactory() - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- getFalseLabel() - Method in class etomica.action.ActionToggle
-
- getFalseLabel() - Method in class etomica.graphics.DeviceToggleButton
-
- getFalseLabel() - Method in class etomica.graphics.DeviceToggleRadioButtons
-
- getFieldColorMap() - Method in class etomica.graph.engine.impl.ConstructorColoredImpl
-
- getFieldColorMap() - Method in interface etomica.graph.engine.Parser.ConstructorColored
-
- getFieldNodes() - Method in class etomica.graph.engine.impl.ConstructorMonoImpl
-
- getFieldNodes() - Method in interface etomica.graph.engine.Parser.ConstructorMono
-
- getFigs() - Method in class g3dsys.control.G3DSys
-
For use only by ImageShell class for iteration
- getFile() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
-
- getFileName() - Method in class etomica.data.DataLogger
-
- getFileName() - Method in class etomica.normalmode.NormalModesMolecular
-
- getFileName() - Method in class etomica.normalmode.NormalModesPotential
-
- getFileNRef(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getFilter() - Method in class etomica.modules.droplet.MeterDeformation
-
- getFirstVector() - Method in class etomica.config.ConformationChainZigZag
-
- getFirstVector() - Method in class etomica.config.ConformationChainZigZag2
-
- getFixedCOM() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- getFixedDeltaU() - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- getFixedDeltaU() - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- getFixedDeltaU() - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- getFixedDeltaU() - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- getFixedSpecies() - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
- getflipcount() - Method in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- getflipfrac() - Method in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- getFluctuationFactor() - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- getFM() - Method in class g3dsys.control.G3DSys
-
Only to be used internally to escape endless delegation
- getFNonAdditiveValues() - Method in class etomica.virial.ClusterSumMultibody
-
- getFont3D(float) - Method in class org.jmol.util.GData
-
- getFont3D(byte) - Static method in class org.jmol.util.JmolFont
-
- getFont3DCurrent() - Method in class org.jmol.g3d.Graphics3D
-
- getFont3DCurrent() - Method in class org.jmol.util.GData
-
- getFont3DFS(String, float) - Method in class org.jmol.util.GData
-
- getFont3DFSS(String, String, float) - Method in class org.jmol.util.GData
-
- getFont3DScaled(JmolFont, float) - Method in class org.jmol.util.GData
-
- getFontAscent(Object) - Method in interface org.jmol.api.ApiPlatform
-
- getFontAscent(Object) - Method in class org.jmol.awt.Platform
-
- getFontDescent(Object) - Method in interface org.jmol.api.ApiPlatform
-
- getFontDescent(Object) - Method in class org.jmol.awt.Platform
-
- getFontFaceID(String) - Static method in class org.jmol.util.JmolFont
-
- getFontFid(float) - Method in class org.jmol.util.GData
-
- getFontFidFS(String, float) - Method in class org.jmol.util.GData
-
- getFontMetrics(JmolFont, Object) - Method in interface org.jmol.api.ApiPlatform
-
- getFontMetrics(JmolFont, Object) - Method in class org.jmol.awt.Platform
-
- getFontStyleID(String) - Static method in class org.jmol.util.GData
-
- getFontStyleID(String) - Static method in class org.jmol.util.JmolFont
-
- getForce() - Method in class etomica.potential.P1HardMovingBoundary
-
- getForceconstant() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getForceconstant() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getForceDimension() - Method in class etomica.potential.P1HardMovingBoundary
-
- getForceSum() - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- getFp8ShadeIndex(float, float, float) - Static method in class org.jmol.util.Shader
-
- getfr(Potential2SoftSpherical, int, double, double) - Static method in class etomica.virial.B2ForSphericallySymmetricUByTrapezoidRule
-
- getfr(int, double, double, double, int, boolean) - Static method in class etomica.virial.B2Ionic
-
- getfr(Potential2SoftSpherical, int, double, double) - Static method in class etomica.virial.B3ForSphericallySymmetricU
-
- getfr(int, double, double) - Static method in class etomica.virial.B3LJ
-
Returns a discretized f function containing N points with a
separation interval of del_r
- getfr(int, double, double) - Static method in class etomica.virial.B4FFTLJ
-
- getfr(int, double, double) - Static method in class etomica.virial.B5FFTLJ
-
- getfr(int, double, double) - Static method in class etomica.virial.B6FFTLJ
-
- getfr(int, double, double) - Static method in class etomica.virial.BnHNCLJ
-
- getfr(int, double, double, Potential2Spherical) - Static method in class etomica.virial.BnIETP2Spherical
-
- getfr(int, double, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnPY_1QC_Helium
-
- getfr(Potential2Spherical, int, double, double, double) - Static method in class etomica.virial.BnPYCHe
-
- getfr(int, double, double) - Static method in class etomica.virial.BnPYLJ
-
- getfr(int, double, double) - Static method in class etomica.virial.BnSCALJ
-
- getfr(IFunction) - Method in class etomica.virial.CalcFFT
-
- getFrac() - Method in class etomica.normalmode.MCMoveHarmonicEin
-
- getFrac() - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- getFrac() - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- getFrequencies() - Method in class etomica.action.CalcVibrationalModes
-
Calculates the frequencies (omegas) of wave vectors described by the eigenvalues (lambdas) of
our system.
- getFrequency(MCMove) - Method in class etomica.integrator.mcmove.MCMoveManager
-
Returns the trial frequency set for the given move, over and above the
move's nominal frequency.
- getFromBinFile(String) - Static method in class etomica.normalmode.ArrayReader2D
-
Deserializes a 3D array from the given file.
- getFromFile(String, int) - Static method in class etomica.eigenstuff.ReaderIn
-
- getFromFile(String) - Static method in class etomica.math.numerical.ArrayReader1D
-
- getFromFile(String, boolean) - Static method in class etomica.math.numerical.ArrayReader1D
-
- getFromFile(String) - Static method in class etomica.normalmode.ArrayReader1D
-
- getFromFile(String, boolean) - Static method in class etomica.normalmode.ArrayReader1D
-
- getFromFile(String) - Static method in class etomica.normalmode.ArrayReader2D
-
Returns 2D arrays from the given file.
- getFromFile(String, int) - Static method in class etomica.normalmode.ArrayReader2D
-
Returns 2D arrays from the given file.
- getFromNode(byte) - Method in interface etomica.graph.model.Graph
-
- getFromNode(byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- getFType() - Method in class etomica.virial.Species7SiteRigidSF6
-
- getFugacityFraction(int) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
- getFugacityFraction() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
Accessor method for the set of fugacity fractions.
- getFullBondMask() - Method in class etomica.virial.ClusterSumHS
-
- getFullBondMask() - Method in interface etomica.virial.ClusterWheatley
-
Returns number bond mask for all points for the configuration passed to
checkConfig
- getFullBondMask() - Method in class etomica.virial.ClusterWheatleyHS
-
- getFullBondMask() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- getFullOverlapResultForAlpha(double) - Method in class etomica.virial.overlap.DataVirialOverlap
-
Returns the full set of overlap results (averages and uncertainties for
target and reference overlap averages).
- getFullRatioResultForAlpha(double) - Method in class etomica.virial.overlap.DataVirialOverlap
-
Returns the full set of ratio results (reference and target ratios and
errors on those ratios).
- getFullRatioResultForAlpha(double, int) - Method in class etomica.virial.overlap.DataVirialOverlap
-
- getFullScreenDimensions(Object, int[]) - Method in interface org.jmol.api.ApiPlatform
-
- getFullScreenDimensions(Object, int[]) - Method in class org.jmol.awt.Platform
-
- getFullSystemResult() - Method in class etomica.virial.overlap.DataVirialOverlap
-
Simply return the reference and target averages and uncertainties.
- getFullSystemResult(int) - Method in class etomica.virial.overlap.DataVirialOverlap
-
- getFunction() - Method in class etomica.data.DataSourceFunction
-
- getFunction() - Method in class etomica.modifier.ModifierFunctionWrapper
-
- getFValues() - Method in class etomica.virial.ClusterSum
-
- getFValues() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- getFValues() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- getFValues() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- getG() - Method in class etomica.modules.droplet.P1Smash
-
- getG1() - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getG1() - Method in interface etomica.graph.isomorphism.SearchState
-
- getG2() - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getG2() - Method in interface etomica.graph.isomorphism.SearchState
-
- getG3D() - Method in class g3dsys.control.G3DSys
-
Get G3D
- getG3DSys() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- getGamma() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- getGamma() - Method in class etomica.potential.P3BondAngleDreiding
-
Returns the characteristic energy of the potential
- getGaussian() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- getGaussian() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- getGaussian() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
-
- getGData() - Method in class org.jmol.g3d.Graphics3D
-
underlying GData object handles all general graphics setup.
- getGlobalMoveInterval() - Method in class etomica.integrator.IntegratorManagerMC
-
Accessor method for the average interval between box-swap trials.
- getGoal() - Method in class etomica.graph.traversal.AbstractTraversal
-
- getGraphics() - Method in class etomica.graphics.EtomicaPlot
-
- getGraphics(Object) - Method in interface org.jmol.api.ApiPlatform
-
- getGraphics(Object) - Method in class org.jmol.awt.Platform
-
- getGroup3Count() - Static method in class org.jmol.viewer.JmolConstants
-
- getGroup3List() - Static method in class org.jmol.viewer.JmolConstants
-
- getGroupID(int[], int) - Static method in class etomica.virial.cluster.VirialDiagrams
-
- getGroupID(int[], int) - Static method in class etomica.virial.cluster.VirialDiagramsPT
-
- getGroupingSize() - Method in class etomica.util.ScientificFormat
-
- getGSum() - Method in class etomica.data.meter.PotentialCalculationRDF
-
- getH() - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- getH() - Method in class etomica.math.numerical.FiniteDifferenceDerivative
-
- getH() - Method in class etomica.spin.P1MagneticField
-
- getH(int) - Method in class etomica.virial.cluster.ClusterOperations
-
Returns all diagrams of order n in the expansion for the total correlation function h(r), in the presence
of any approximations currently in effect.
- getHarmonicEnergy() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- getHashmapAtomsetIterator() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- getHashMapAtomTypeLikePairs() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- getHashMapAtomTypesUnlikePairs() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- getHashMapPotentialIntraBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- getHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- getHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- getHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.HashMapPotentialNonBonded
-
- getHeight() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getHeight() - Method in class org.jmol.util.JmolFont
-
- getHello() - Method in class etomica.server.EtomicaServerConfig
-
- getHelmholtzFreeEnergy(double) - Method in class etomica.normalmode.HarmonicCrystal
-
- getHelmholtzFreeEnergy(double) - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
-
- getHelmholtzFreeEnergy(double) - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
-
- getHelmholtzFreeEnergy(double) - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
-
- getHermiteList(int, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f, Tuple3f[], int, int, boolean) - Static method in class org.jmol.util.Hermite
-
- getHexCode(short) - Static method in class org.jmol.util.Colix
-
- getHexCodes(short[]) - Static method in class org.jmol.util.Colix
-
- getHexColorFromRGB(int) - Static method in class org.jmol.util.Escape
-
- getHexitValue(char) - Static method in class org.jmol.util.Escape
-
- getHistogram() - Method in interface etomica.data.histogram.Histogram
-
Returns the histogram as an array of doubles
- getHistogram() - Method in class etomica.data.histogram.HistogramCollapsing
-
- getHistogram() - Method in class etomica.data.histogram.HistogramDiscrete
-
- getHistogram() - Method in class etomica.data.histogram.HistogramNotSoSimple
-
- getHistogram() - Method in class etomica.data.histogram.HistogramReweightedData
-
- getHistogram() - Method in class etomica.data.histogram.HistogramSimple
-
- getHistogram() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- getHistogram() - Method in class etomica.mappedvirial.MeterMeanForce
-
- getHistogram2() - Method in class etomica.mappedvirial.MeterMeanForce
-
- getHistograms() - Method in class etomica.data.AccumulatorHistogram
-
- getHistory() - Method in class etomica.data.AccumulatorHistory
-
- getHistory() - Method in interface etomica.data.history.History
-
Returns an array containing the y values that have been added to the
History.
- getHistory() - Method in class etomica.data.history.HistoryCollapsing
-
Returns the history
- getHistory() - Method in class etomica.data.history.HistoryComplete
-
Returns an the history
- getHistory() - Method in class etomica.data.history.HistoryScrolling
-
Returns an array with the most recent history at the end.
- getHistoryLength() - Method in interface etomica.data.history.History
-
Returns the number of data points tracked by the History.
- getHistoryLength() - Method in class etomica.data.history.HistoryCollapsing
-
- getHistoryLength() - Method in class etomica.data.history.HistoryComplete
-
- getHistoryLength() - Method in class etomica.data.history.HistoryScrolling
-
- getHorizGBC() - Static method in class etomica.graphics.SimulationPanel
-
- getHpType() - Method in class etomica.paracetamol.SpeciesParacetamol
-
- getHType() - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- getHType() - Method in class etomica.AlkaneEH.SpeciesMethane
-
- getHType() - Method in class etomica.models.OPLS.SpeciesAceticAcid
-
- getHType() - Method in class etomica.models.traPPE.SpeciesMethanol
-
- getHType() - Method in class etomica.virial.SpeciesMethane
-
- getHybridAcceptance() - Method in class etomica.integrator.IntegratorMD
-
- getHydrogenType() - Method in class etomica.models.rowley.SpeciesEthanol
-
- getHydrogenType() - Method in class etomica.models.rowley.SpeciesMethanol
-
- getHydrogenType() - Method in class etomica.models.water.SpeciesWater3P
-
- getHydrogenType() - Method in class etomica.models.water.SpeciesWater3POriented
-
- getHydrogenType() - Method in class etomica.models.water.SpeciesWater4P
-
- getHydrogenType() - Method in class etomica.models.water.SpeciesWater4PCOM
-
- getHydrogenType() - Method in class etomica.models.water.SpeciesWater4POriented
-
- getHydrophobicity(int) - Static method in class org.jmol.util.Elements
-
- getHyType() - Method in class etomica.paracetamol.SpeciesParacetamol
-
- getICPYCorrection(byte, boolean) - Static method in class etomica.virial.PYGenerator
-
- getId() - Method in interface etomica.graph.model.Edge
-
- getId() - Method in class etomica.graph.model.impl.EdgeImpl
-
- getId() - Method in class etomica.graph.model.impl.NodeImpl
-
- getId() - Method in interface etomica.graph.model.Node
-
- getId(Object) - Method in class etomica.meta.SimulationModel
-
- getId() - Method in class etomica.server.representations.PropertyUpdate
-
- getID() - Method in class etomica.virial.CoordinatePairLeafSet
-
- getID() - Method in class etomica.virial.CoordinatePairMoleculeSet
-
- getID() - Method in interface etomica.virial.CoordinatePairSet
-
- getId() - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
-
- getId() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getId() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getId() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getId() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getId() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getId() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getId() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getId() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getId() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getId() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getID() - Method in class g3dsys.images.Figure
-
Get the ID of the figure
- getIDataInfo(int) - Method in class etomica.normalmode.MeterTiltRotationHistogram
-
- getIdealRefFraction(double) - Method in class etomica.overlap.DataOverlap
-
Returns the ideal fraction of time (or steps) spent in the reference
system under the assumption that the current data while spending
oldFrac amount of the calculation on the reference system.
- getIdealRefFraction(double) - Method in interface etomica.overlap.IntegratorOverlap.ReferenceFracSource
-
- getIdealRefFraction(double) - Method in class etomica.virial.overlap.DataSourceVirialOverlap
-
- getIdealRefFraction(double) - Method in class etomica.virial.overlap.DataVirialOverlap
-
- getIdealRefStepFraction() - Method in class etomica.overlap.IntegratorOverlap
-
- getIgnoredAtomType() - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- getImageHeight(Object) - Method in interface org.jmol.api.ApiPlatform
-
- getImageHeight(Object) - Method in class org.jmol.awt.Platform
-
- getImagEigenvalues() - Method in class etomica.eigenstuff.MyEigenvalueDecomposition
-
Return the imaginary parts of the eigenvalues
- getImagEigenvalues() - Method in class org.jmol.util.Eigen
-
Return the imaginary parts of the eigenvalues
- getImageShells() - Method in class etomica.graphics.DisplayBox
-
- getImageWidth(Object) - Method in interface org.jmol.api.ApiPlatform
-
- getImageWidth(Object) - Method in class org.jmol.awt.Platform
-
- getImaginary() - Method in class etomica.math.numerical.FastFourierTransform
-
- getImax() - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- getIncludeHeader() - Method in class etomica.data.DataArrayWriter
-
Returns whether the writer includes column headers or not
- getIncludeHeader() - Method in class etomica.data.DataTableWriter
-
Returns whether the writer includes column headers or not
- getIndependentArrayDimension() - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getIndependentArrayDimension() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getIndependentArrayDimension() - Method in class etomica.data.DataSourceFunction
-
- getIndependentArrayDimension() - Method in interface etomica.data.DataSourceIndependent
-
Returns the number of independent data dimensions
- getIndependentArrayDimension() - Method in class etomica.data.DataSourceIndependentSimple
-
- getIndependentArrayDimension() - Method in class etomica.data.DataSourcePoints
-
- getIndependentArrayDimension() - Method in class etomica.data.DataSourceRmsVelocity
-
- getIndependentArrayDimension() - Method in class etomica.data.meter.MeterDihedralAngle
-
- getIndependentArrayDimension() - Method in class etomica.data.meter.MeterProfile
-
- getIndependentArrayDimension() - Method in class etomica.data.meter.MeterProfileByAtoms
-
- getIndependentArrayDimension() - Method in class etomica.data.meter.MeterProfileByVolume
-
- getIndependentArrayDimension() - Method in class etomica.data.meter.MeterRDF
-
- getIndependentArrayDimension() - Method in class etomica.data.meter.MeterRDFPC
-
- getIndependentArrayDimension() - Method in class etomica.data.meter.MeterStructureFactor
-
- getIndependentArrayDimension() - Method in class etomica.mappedRdf.MeterMappedRdf
-
- getIndependentArrayDimension() - Method in class etomica.mappedvirial.MeterMeanForce
-
- getIndependentArrayDimension() - Method in class etomica.metastable.DataProcessorXY
-
- getIndependentArrayDimension() - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- getIndependentArrayDimension() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getIndependentArrayDimension() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentArrayDimension() - Method in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourceFE
-
- getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourceFEHistogram
-
- getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourceImposedFEFit
-
- getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourceImposedFEHistogram
-
- getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourcePMu
-
- getIndependentArrayDimension() - Method in class etomica.normalmode.DataSourcePN
-
- getIndependentArrayDimension() - Method in class etomica.normalmode.MeterAtomicDisplacement
-
- getIndependentArrayDimension() - Method in class etomica.normalmode.MeterTiltHistogram
-
- getIndependentArrayDimension() - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- getIndependentData(int) - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getIndependentData(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getIndependentData(int) - Method in class etomica.data.DataSourceFunction
-
- getIndependentData(int) - Method in interface etomica.data.DataSourceIndependent
-
Returns the X data for the given dimension
- getIndependentData(int) - Method in class etomica.data.DataSourceIndependentSimple
-
- getIndependentData(int) - Method in class etomica.data.DataSourcePoints
-
- getIndependentData(int) - Method in class etomica.data.DataSourceRmsVelocity
-
- getIndependentData(int) - Method in class etomica.data.meter.MeterDihedralAngle
-
- getIndependentData(int) - Method in class etomica.data.meter.MeterProfile
-
- getIndependentData(int) - Method in class etomica.data.meter.MeterProfileByAtoms
-
- getIndependentData(int) - Method in class etomica.data.meter.MeterProfileByVolume
-
- getIndependentData(int) - Method in class etomica.data.meter.MeterRDF
-
- getIndependentData(int) - Method in class etomica.data.meter.MeterRDFPC
-
- getIndependentData(int) - Method in class etomica.data.meter.MeterStructureFactor
-
- getIndependentData(int) - Method in class etomica.mappedRdf.MeterMappedRdf
-
- getIndependentData(int) - Method in class etomica.mappedvirial.MeterMeanForce
-
- getIndependentData(int) - Method in class etomica.metastable.DataProcessorXY
-
- getIndependentData(int) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- getIndependentData(int) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- getIndependentData(int) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- getIndependentData(int) - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- getIndependentData(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- getIndependentData(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getIndependentData(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentData(int) - Method in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- getIndependentData(int) - Method in class etomica.normalmode.DataSourceFE
-
- getIndependentData(int) - Method in class etomica.normalmode.DataSourceFEHistogram
-
- getIndependentData(int) - Method in class etomica.normalmode.DataSourceImposedFEFit
-
- getIndependentData(int) - Method in class etomica.normalmode.DataSourceImposedFEHistogram
-
- getIndependentData(int) - Method in class etomica.normalmode.DataSourcePMu
-
- getIndependentData(int) - Method in class etomica.normalmode.DataSourcePN
-
- getIndependentData(int) - Method in class etomica.normalmode.MeterAtomicDisplacement
-
- getIndependentData(int) - Method in class etomica.normalmode.MeterTiltHistogram
-
- getIndependentData(int) - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- getIndependentDataInfo(int) - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getIndependentDataInfo(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getIndependentDataInfo(int) - Method in class etomica.data.DataSourceFunction
-
- getIndependentDataInfo(int) - Method in interface etomica.data.DataSourceIndependent
-
Returns the DataInfo for the given dimension
- getIndependentDataInfo(int) - Method in class etomica.data.DataSourceIndependentSimple
-
- getIndependentDataInfo(int) - Method in class etomica.data.DataSourcePoints
-
- getIndependentDataInfo(int) - Method in class etomica.data.DataSourceRmsVelocity
-
- getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterDihedralAngle
-
- getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterProfile
-
- getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterProfileByAtoms
-
- getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterProfileByVolume
-
- getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterRDF
-
- getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterRDFPC
-
- getIndependentDataInfo(int) - Method in class etomica.data.meter.MeterStructureFactor
-
- getIndependentDataInfo(int) - Method in class etomica.mappedRdf.MeterMappedRdf
-
- getIndependentDataInfo(int) - Method in class etomica.mappedvirial.MeterMeanForce
-
- getIndependentDataInfo(int) - Method in class etomica.metastable.DataProcessorXY
-
- getIndependentDataInfo(int) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- getIndependentDataInfo(int) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getIndependentDataInfo(int) - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentDataInfo(int) - Method in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourceFE
-
- getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourceFEHistogram
-
- getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourceImposedFEFit
-
- getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourceImposedFEHistogram
-
- getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourcePMu
-
- getIndependentDataInfo(int) - Method in class etomica.normalmode.DataSourcePN
-
- getIndependentDataInfo(int) - Method in class etomica.normalmode.MeterAtomicDisplacement
-
- getIndependentDataInfo(int) - Method in class etomica.normalmode.MeterTiltHistogram
-
- getIndependentDataInfo(int) - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- getIndependentTag() - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getIndependentTag() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getIndependentTag() - Method in class etomica.data.DataSourceFunction
-
- getIndependentTag() - Method in interface etomica.data.DataSourceIndependent
-
Returns the tag associated with this DataSource.
- getIndependentTag() - Method in class etomica.data.DataSourceIndependentSimple
-
- getIndependentTag() - Method in class etomica.data.DataSourcePoints
-
- getIndependentTag() - Method in class etomica.data.DataSourceRmsVelocity
-
- getIndependentTag() - Method in class etomica.data.meter.MeterDihedralAngle
-
- getIndependentTag() - Method in class etomica.data.meter.MeterProfile
-
- getIndependentTag() - Method in class etomica.data.meter.MeterProfileByAtoms
-
- getIndependentTag() - Method in class etomica.data.meter.MeterProfileByVolume
-
- getIndependentTag() - Method in class etomica.data.meter.MeterRDF
-
- getIndependentTag() - Method in class etomica.data.meter.MeterRDFPC
-
- getIndependentTag() - Method in class etomica.data.meter.MeterStructureFactor
-
- getIndependentTag() - Method in class etomica.mappedRdf.MeterMappedRdf
-
- getIndependentTag() - Method in class etomica.mappedvirial.MeterMeanForce
-
- getIndependentTag() - Method in class etomica.metastable.DataProcessorXY
-
- getIndependentTag() - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- getIndependentTag() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- getIndependentTag() - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- getIndependentTag() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- getIndependentTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- getIndependentTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getIndependentTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getIndependentTag() - Method in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- getIndependentTag() - Method in class etomica.normalmode.DataSourceFE
-
- getIndependentTag() - Method in class etomica.normalmode.DataSourceFEHistogram
-
- getIndependentTag() - Method in class etomica.normalmode.DataSourceImposedFEFit
-
- getIndependentTag() - Method in class etomica.normalmode.DataSourceImposedFEHistogram
-
- getIndependentTag() - Method in class etomica.normalmode.DataSourcePMu
-
- getIndependentTag() - Method in class etomica.normalmode.DataSourcePN
-
- getIndependentTag() - Method in class etomica.normalmode.MeterAtomicDisplacement
-
- getIndependentTag() - Method in class etomica.normalmode.MeterTiltHistogram
-
- getIndependentTag() - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- getIndex() - Method in class etomica.atom.Atom
-
- getIndex(IAtom) - Method in class etomica.atom.AtomToAtomSetFixed
-
- getIndex(IAtom) - Method in interface etomica.atom.AtomToIndex
-
Returns an integer that this instance associates with the given atom.
- getIndex(IAtom) - Method in class etomica.atom.AtomToIndexChild
-
- getIndex() - Method in class etomica.atom.AtomType
-
- getIndex() - Method in interface etomica.atom.IAtom
-
- getIndex() - Method in class etomica.box.Box
-
- getIndex() - Method in class etomica.box.BoxAtomIndexEvent
-
- getIndex() - Method in class etomica.box.BoxIndexEvent
-
- getIndex() - Method in class etomica.box.BoxMoleculeIndexEvent
-
- getIndex() - Method in interface etomica.data.DataDistributer.Indexer
-
- getIndex(double) - Method in class etomica.data.DataSourceUniform
-
Returns the index of the x value closest to the argument.
- getIndex() - Method in interface etomica.molecule.IMolecule
-
Returns this IMolecule's index, which is its place in the list of
molecules of its ISpecies in its Box.
- getIndex() - Method in class etomica.molecule.Molecule
-
- getIndex(IMolecule) - Method in interface etomica.molecule.MoleculeToIndex
-
Returns an integer that this instance associates with the given atom.
- getIndex(IMolecule) - Method in class etomica.molecule.MoleculeToMoleculeListSpecies
-
- getIndex(IMolecule) - Method in class etomica.molecule.MoleculeToMoleculeSetFixed
-
- getIndex() - Method in class etomica.simulation.SimulationAtomTypeIndexEvent
-
- getIndex() - Method in class etomica.simulation.SimulationIndexEvent
-
- getIndex() - Method in class etomica.simulation.SimulationSpeciesIndexEvent
-
- getIndex() - Method in interface etomica.species.ISpecies
-
Returns the index for this ISpecies, within the context of an Simulation.
- getIndex() - Method in class etomica.species.Species
-
- getIndexed() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getIndexIterator() - Method in class etomica.space.Boundary
-
- getIndexIterator() - Method in class etomica.space.BoundaryDeformablePeriodic
-
- getIndexIterator() - Method in class etomica.space.BoundaryRectangularNonperiodic
-
- getIndexIterator() - Method in class etomica.space.BoundaryRectangularPeriodic
-
- getIndexIterator() - Method in class etomica.space.BoundaryRectangularPore
-
- getIndexIterator() - Method in class etomica.space.BoundaryRectangularSlit
-
- getIndexIterator() - Method in class etomica.space3d.BoundaryTruncatedOctahedron
-
- getIndexSelectedSpecies() - Method in exception etomica.virial.GUI.components.ExceptionDoNotRemoveSpecies
-
- getInflateDimensions() - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
Accessor method for setInflateDimension.
- getInfo() - Method in class org.jmol.util.Quaternion
-
- getInnerIterator() - Method in class etomica.atom.iterator.ApiInnerVariable
-
Accessor method for the inner-loop atom iterator.
- getInnerIterator() - Method in class etomica.atom.iterator.ApiIntergroup
-
Accessor method for the inner-loop atom iterator.
- getInnerIterator() - Method in class etomica.graph.iterators.CartesianIterator
-
- getInnerIterator() - Method in class etomica.molecule.iterator.MpiInnerFixed
-
Accessor method for the inner-loop atom iterator.
- getInnerIterator() - Method in class etomica.molecule.iterator.MpiInnerVariable
-
Accessor method for the inner-loop atom iterator.
- getInnerList() - Method in class etomica.atom.iterator.ApiInterArrayList
-
Returns the inner list used to generate the pairs.
- getInnerList() - Method in class etomica.molecule.iterator.MpiInterArrayList
-
Returns the inner list used to generate the pairs.
- getInnerPermutator() - Method in class etomica.graph.iterators.CartesianPermutator
-
- getInnerRadius() - Method in class etomica.atom.AtomTypeSpheroPolyhedron
-
- getInnerRadius() - Method in class etomica.normalmode.P1Constraint
-
- getInputFileName() - Method in class etomica.util.ReadParameters
-
Returns the fileName parameters are read from.
- getInputFileName() - Method in class etomica.util.WriteParameters
-
Returns the fileName parameters are read from.
- getInstance(int) - Static method in class etomica.space.Space
-
- getInstance() - Static method in class etomica.space1d.Space1D
-
- getInstance() - Static method in class etomica.space2d.Space2D
-
- getInstance() - Static method in class etomica.space3d.Space3D
-
- getInstance() - Static method in class etomica.virial.GUI.components.HashMapPotentialNonBonded
-
- getInstance() - Static method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- getInstance() - Static method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
-
- getInstances() - Method in class etomica.server.resources.SimulationsIndexResource
-
- getIntegrator() - Method in class etomica.action.ActionIntegrate
-
- getIntegrator() - Method in class etomica.action.activity.ActivityIntegrate
-
- getIntegrator() - Method in interface etomica.action.IntegratorAction
-
- getIntegrator() - Method in class etomica.action.IntegratorActionAdapter
-
- getIntegrator() - Method in class etomica.data.DataSourceTensorVirialHard
-
- getIntegrator() - Method in class etomica.data.meter.MeterKineticEnergyFromIntegrator
-
- getIntegrator() - Method in class etomica.data.meter.MeterPotentialEnergyFromIntegrator
-
- getIntegrator() - Method in class etomica.data.meter.MeterPressure
-
Returns the integrator associated with this instance.
- getIntegrator() - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
Returns the integrator associated with this instance.
- getIntegrator() - Method in class etomica.data.meter.MeterPressureHard
-
- getIntegrator() - Method in class etomica.data.meter.MeterPressureHardTensor
-
- getIntegrator() - Method in class etomica.data.meter.MeterPressureMolecular
-
Returns the integrator associated with this instance.
- getIntegrator() - Method in class etomica.data.meter.MeterPressureTensorFromIntegrator
-
- getIntegrator() - Method in class etomica.data.meter.MeterWidomInsertion
-
Returns the integrator associated with this class.
- getIntegrator() - Method in class etomica.integrator.IntegratorEvent
-
- getIntegrator() - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Returns the integrator associated with this class.
- getIntegrator() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- getIntegrator() - Method in class etomica.modules.mu.DataSourceWallPressureMu
-
- getIntegrator() - Method in class etomica.normalmode.MeterPressureSuperBox
-
Returns the integrator associated with this instance.
- getIntegrator() - Method in class etomica.simulation.Simulation
-
- getIntegrator() - Method in class etomica.thermointegration.LjMc3D
-
- getIntegratorMC() - Method in class etomica.integrator.IntegratorMD
-
- getIntegratorOverlap() - Method in class etomica.normalmode.SimOverlapModule
-
- getIntegrators() - Method in class etomica.integrator.IntegratorManagerMC
-
- getInteractingList() - Method in class etomica.nbr.list.AtomPotentialList
-
Returns booleans indicating whether the Atom interacts with each potential or not.
- getInteractingList() - Method in class etomica.nbr.list.molecule.MoleculePotentialList
-
Returns booleans indicating whether the Atom interacts with each
potential or not.
- getInteractionRange() - Method in class etomica.nbr.CriterionPositionWall
-
Returns the interaction range of the wall potential.
- getInteractionRange() - Method in class etomica.nbr.CriterionSimple
-
- getInteractionRange() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- getInteractionRangeDimension() - Method in class etomica.nbr.CriterionPositionWall
-
- getInteractionRangeDimension() - Method in class etomica.nbr.CriterionSimple
-
- getInteractionRangeDimension() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- getInteriorColor() - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
-
- getIntermolecularPotential() - Method in class etomica.parser.ParmedStructure
-
Gets the intermolecular
PotentialGroup for the atom types found in this Structure.
- getIntersection(Point3f, Vector3f, Point4f, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- getIntersection(float, Point4f, Point3f[], List<Point3f[]>, float[], BitSet, MeshSurface, boolean, boolean, int, boolean) - Method in class org.jmol.util.MeshSurface
-
- getIntersectionPP(Point4f, Point4f) - Static method in class org.jmol.util.Measure
-
- getInterval() - Method in class etomica.data.DataPumpListener
-
- getInterval() - Method in class etomica.data.DataPumpListenerPow
-
- getInterval() - Method in class etomica.data.DataPumpListenerPowStrict
-
- getInterval() - Method in class etomica.integrator.IntegratorListenerAction
-
- getIntialdisplaylist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getIntialpotentialdisplaylist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getIntraMolecularCriterion() - Method in class etomica.nbr.CriterionInterMolecular
-
Returns the intramolecular criterion, or null if none is in use.
- getIntraPotentials(ISpecies) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- getIntraPotentials(ISpecies) - Method in class etomica.nbr.PotentialMasterNbr
-
- getInverseNormix(short) - Static method in class org.jmol.util.Normix
-
- getIsFluctuationFromAvg() - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- getIsNewPair(int[]) - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- getIsNewPair(int[]) - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- getIsothermalButtonsVisibility() - Method in class etomica.graphics.DeviceThermoSlider
-
- getIsothermalButtonsVisibility() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- getIsotopeNumber(short) - Static method in class org.jmol.util.Elements
-
- getIterator() - Method in class etomica.chem.models.Model.PotentialAndIterator
-
- getIterator() - Method in class etomica.data.DataSourceRmsVelocity
-
- getIterator() - Method in class etomica.data.meter.MeterKineticEnergy
-
Returns the iterator that defines the atoms summed for their
kinetic energy.
- getIterator() - Method in class etomica.data.meter.MeterLocalDensity
-
- getIterator() - Method in class etomica.data.meter.MeterLocalMoleFraction
-
- getIterator() - Method in class etomica.data.meter.MeterRadiusGyration
-
Accessor method for the iterator that generates the atom pairs used to
tabulate the ROG
- getIterator() - Method in class etomica.lattice.LatticeSum
-
- getIterator() - Method in class etomica.lattice.LatticeSumCrystal
-
- getIterator() - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- getIterator() - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
- getIy() - Method in class etomica.math.numerical.AkimaSplineSmootherDy
-
calculate the cumulative integral of y, interpolating dy/dx with a
spline curve
- getJacobian() - Method in class etomica.normalmode.CalcJacobian
-
- getJavaInitializationString() - Method in class etomica.graphics.DimensionedDoubleEditor
-
Returns value in simulation units.
- getJmax() - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- getJSpinnerCountOfSpecies(int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getJump() - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
-
- getJump() - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
-
- getK() - Method in class etomica.lattice.LatticeSum
-
- getK() - Method in class etomica.lattice.LatticeSumCrystal
-
- getK() - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- getK() - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
- getKappa() - Method in class etomica.yukawa.P2Yukawa
-
Accessor methods for size and energy parameters.
- getKinetic() - Method in class etomica.data.meter.MeterEnergy
-
- getKineticEnergy() - Method in class etomica.data.meter.MeterEnergy
-
- getKineticEnergy() - Method in class etomica.integrator.IntegratorMD
-
- getLabel() - Method in class etomica.action.ActionToggle
-
Returns the true or false label, depending on the current state of the
toggle.
- getLabel() - Method in class etomica.data.DataInfo
-
- getLabel() - Method in class etomica.data.DataInfoFactory
-
Returns the label
- getLabel() - Method in interface etomica.data.IDataInfo
-
- getLabel() - Method in interface etomica.data.IDataInfoFactory
-
Returns the label
- getLabel() - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- getLabel() - Method in class etomica.graphics.DeviceBox
-
- getLabel() - Method in class etomica.graphics.DeviceButton
-
- getLabel() - Method in class etomica.graphics.DeviceSelector
-
- getLabel() - Method in class etomica.graphics.DeviceSlider
-
- getLabel() - Method in class etomica.graphics.DeviceSpinner
-
- getLabel() - Method in class etomica.graphics.DeviceThermoSelector
-
- getLabel() - Method in class etomica.graphics.Display
-
Accessor method of the label describing the display.
- getLabel() - Method in class etomica.graphics.DisplayTextBox
-
- getLabel() - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- getLabel() - Method in interface etomica.modifier.Modifier
-
Returns a descriptive label of the property being modified.
- getLabel() - Method in class etomica.modifier.ModifierGeneral
-
- getLabel() - Method in class etomica.modifier.ModifierNMolecule
-
- getLabel() - Method in class etomica.modules.adsorption.ModifierPMu
-
- getLabel() - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
-
- getLabel() - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
-
- getLabel() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
-
- getLabel() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
-
- getLabel() - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- getLabel() - Method in class etomica.modules.entropylottery.ModifierDimensions
-
- getLabel() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- getLabel() - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- getLabel() - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- getLabel() - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- getLabel() - Method in class etomica.modules.pistoncylinder.ActionPistonUpdate
-
- getLabel() - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
-
- getLabel() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
-
- getLabel() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
-
- getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
-
- getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
-
- getLabel() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- getLabel() - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
-
- getLabel() - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
-
- getLabel() - Method in class etomica.normalmode.ModifierCells3D
-
- getLabel() - Method in class etomica.normalmode.ModifierXCells2D
-
- getLabel() - Method in class etomica.normalmode.ModifierYCells2D
-
- getLabel() - Method in class etomica.virial.simulations.ModifierTPI
-
- getLabel() - Method in class etomica.zeolite.DeviceButtonSingle
-
- getLabelPosition() - Method in class etomica.graphics.DeviceBox
-
- getLabelPosition() - Method in class etomica.graphics.DisplayTextBox
-
- getLabelType() - Method in class etomica.graphics.DeviceBox
-
- getLabelType() - Method in class etomica.graphics.DisplayTextBox
-
- getLambda() - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Accessor method for well-diameter multiplier.
- getLambda() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Accessor method for well-diameter multiplier.
- getLambda() - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Accessor method for well-diameter multiplier.
- getLambda() - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Accessor method for well-diameter multiplier.
- getLambda() - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- getLambda() - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- getLambda() - Method in class etomica.potential.P2DoubleWell
-
Accessor method for well-diameter multiplier.
- getLambda() - Method in class etomica.potential.P2PenetrableSquareWell
-
Accessor method for well-diameter multiplier.
- getLambda() - Method in class etomica.potential.P2SquareWell
-
Accessor method for well-diameter multiplier.
- getLambda() - Method in class etomica.potential.P2SquareWellRobust
-
Accessor method for well-diameter multiplier.
- getLambda() - Method in class etomica.potential.P2TriangleWell
-
- getLambdaDimension() - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- getLambdaDimension() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- getLambdaDimension() - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
- getLambdaDimension() - Method in class etomica.modules.mu.P2SquareWellOneSide
-
- getLambdaDimension() - Method in class etomica.potential.P2DoubleWell
-
- getLambdaDimension() - Method in class etomica.potential.P2PenetrableSquareWell
-
- getLambdaDimension() - Method in class etomica.potential.P2SquareWell
-
- getLambdaDimension() - Method in class etomica.potential.P2SquareWellRobust
-
- getLambdaDimension() - Method in class etomica.potential.P2TriangleWell
-
- getLambdas() - Method in class etomica.action.CalcVibrationalModes
-
Performs an eigenvalue decomposition of the NxN matrix, fC.
- getLanguage() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getLastA() - Method in class etomica.normalmode.WriteS
-
- getLastBestParam() - Method in class etomica.modules.interfacial.FitTanh
-
- getLastBestParam() - Method in class etomica.surfacetension.FitTanh
-
- getLastCPairID() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- getLastDMu() - Method in class etomica.normalmode.DataSourceMuRoot
-
- getLastDPressure() - Method in class etomica.normalmode.DataSourceMuRoot
-
- getLastDPressure() - Method in class etomica.normalmode.DataSourceMuRootPMatch
-
- getLastDU() - Method in class etomica.normalmode.DataSourceMuRoot
-
- getLastGamma() - Method in class etomica.math.Gamma
-
Return the normalized complementary incomplete gamma function from the
last calculation.
- getLastGammaStar() - Method in class etomica.math.Gamma
-
Return the normalized incomplete gamma function from the last
calculation.
- getLastLine() - Method in class etomica.graph.engine.ConsoleUI
-
- getLastLnTot() - Method in class etomica.normalmode.DataSourceMuRoot
-
- getLastLnTot() - Method in class etomica.normalmode.DataSourceMuRootPMatch
-
- getLastPolarizationEnergy() - Method in class etomica.models.co2.PNCO2GCPM
-
- getLastPolarizationEnergy() - Method in class etomica.models.co2.PNGCPM
-
- getLastPolarizationEnergy() - Method in class etomica.models.water.PNWaterGCPM
-
- getLastPolarizationEnergy() - Method in interface etomica.potential.PotentialPolarizable
-
Returns the polarization energy from the last call to energy(AtomSet).
- getLastPressure() - Method in class etomica.normalmode.DataSourceMuRoot
-
- getLastPressure() - Method in class etomica.normalmode.DataSourceMuRoot1
-
- getLastPressure() - Method in class etomica.normalmode.DataSourceMuRootPMatch
-
- getLastTotalEnergy() - Method in class etomica.normalmode.MCMoveHarmonic
-
Returns the harmonic energy of the configuration based on the last
harmonic move made by this MC Move.
- getLastVacancyConcentration() - Method in class etomica.normalmode.DataSourceMuRoot
-
- getLastVacancyConcentration() - Method in class etomica.normalmode.DataSourceMuRoot1
-
- getLastVacancyConcentration() - Method in class etomica.normalmode.DataSourceMuRootPMatch
-
- getLastValue() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- getLastValues() - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- getLattice() - Method in interface etomica.box.BoxCellManager
-
Returns the lattice that defines the cell arrangement.
- getLattice() - Method in class etomica.lattice.LatticeSum
-
- getLattice() - Method in class etomica.lattice.LatticeSumCrystal
-
- getLattice() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Returns the lattice from which the iterates are given.
- getLattice() - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- getLattice() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- getLattice() - Method in class etomica.nbr.cell.NeighborCellManager
-
- getLattice() - Method in class etomica.nbr.site.NeighborSiteManager
-
Returns the lattice used to define the neighbor structure.
- getLattice() - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
- getLatticeAMemento() - Method in class etomica.config.GrainBoundaryConfiguration
-
Returns a lattice with positions the same as those used in the
most recent use of initializeCoordinates.
- getLatticeArrayIndex() - Method in class etomica.nbr.cell.Cell
-
- getLatticeArrayIndex() - Method in class etomica.nbr.cell.molecule.CellMolecular
-
- getLatticeArrayIndex() - Method in class etomica.nbr.site.AtomSite
-
- getLatticeBMemento() - Method in class etomica.config.GrainBoundaryConfiguration
-
- getLatticeConstant() - Method in interface etomica.lattice.CubicLattice
-
Accesses the size of the unit cell, the length of each edge of a single cell.
- getLatticeConstant() - Method in class etomica.lattice.LatticeCubicBcc
-
- getLatticeConstant() - Method in class etomica.lattice.LatticeCubicDiamond
-
- getLatticeConstant() - Method in class etomica.lattice.LatticeCubicFcc
-
- getLatticeConstant() - Method in class etomica.lattice.LatticeCubicSimple
-
- getLatticeConstants() - Method in class etomica.config.ConfigurationLattice.MyLattice
-
- getLatticeConstants() - Method in class etomica.lattice.BravaisLattice
-
- getLatticeConstants() - Method in interface etomica.lattice.SpaceLattice
-
- getLatticeConstants() - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
-
- getLatticeConstants() - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
-
- getLatticeCorrec() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- getLatticeEnergy() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- getLatticeEnergy() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- getLatticeEnergy() - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- getLatticeEnergy() - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- getLatticeEnergy() - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- getLatticeEnergy() - Method in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- getLatticeEnergy() - Method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- getLatticeEnergy() - Method in class etomica.normalmode.HarmonicCrystal
-
- getLatticeEnergy() - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
-
- getLatticeEnergy() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- getLatticeEnergy() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- getLatticeEnergy() - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- getLatticeEnergy() - Method in class etomica.normalmode.MeterOverlapSwitch
-
- getLatticeEnergy() - Method in class etomica.normalmode.MeterTargetTP
-
- getLatticeEnergy() - Method in class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
-
- getLatticeEnergy() - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
-
- getLatticeEnergy() - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
-
- getLatticeMemento() - Method in class etomica.config.ConfigurationLattice
-
Returns a lattice with positions the same as those used in the
most recent use of initializeCoordinates.
- getLatticeMemento() - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
Returns a lattice with positions the same as those used in the
most recent use of initializeCoordinates.
- getLatticeMemento() - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
Returns a lattice with positions the same as those used in the
most recent use of initializeCoordinates.
- getLatticePosition(IAtom) - Method in class etomica.normalmode.CoordinateDefinition
-
- getLatticePosition(IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
-
- getLatticePosition(IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- getLayers() - Method in class g3dsys.images.ImageShell
-
Gets the number of image shell layers
- getLeafIndex() - Method in class etomica.atom.Atom
-
- getLeafIndex() - Method in interface etomica.atom.IAtom
-
Returns the global index (within the Box) of this Atom.
- getLeafList() - Method in class etomica.box.Box
-
- getLeafType() - Method in class etomica.species.SpeciesSpheres
-
- getLeafType() - Method in class etomica.species.SpeciesSpheresMono
-
- getLength() - Method in interface etomica.data.IData
-
Returns the number of values held by the data instance.
- getLength() - Method in interface etomica.data.IDataInfo
-
Returns the number of numerical values held by the IData object.
- getLength() - Method in class etomica.data.types.DataDouble.DataInfoDouble
-
- getLength() - Method in class etomica.data.types.DataDouble
-
Returns 1, indicating that this data object holds one value.
- getLength() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
-
Returns the total number of elements in the constructed DataDoubleArray.
- getLength() - Method in class etomica.data.types.DataDoubleArray
-
Returns the total length of the wrapped array.
- getLength() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
-
Returns the total number of elements in the constructed DataDoubleArray.
- getLength() - Method in class etomica.data.types.DataDoubleBDArray
-
Returns the total length of the wrapped array.
- getLength() - Method in class etomica.data.types.DataGroup.DataInfoGroup
-
- getLength() - Method in class etomica.data.types.DataGroup
-
- getLength() - Method in class etomica.data.types.DataTable
-
Returns the number of values held by the data instance.
- getLength() - Method in class etomica.data.types.DataTensor.DataInfoTensor
-
- getLength() - Method in class etomica.data.types.DataTensor
-
Returns the number of elements in the wrapped tensor.
- getLength() - Method in class etomica.data.types.DataVector.DataInfoVector
-
- getLength() - Method in class etomica.data.types.DataVector
-
Returns the number of elements in the wrapped vector.
- getLength() - Method in class etomica.math.geometry.LineSegment
-
- getLengthAlkaneChain(int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- getLevel(int) - Static method in class org.jmol.util.Logger
-
Returns the text corresponding to a level.
- getLightSource() - Static method in class org.jmol.util.GData
-
- getLiquidColor() - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- getLiquidFilter() - Method in class etomica.modules.droplet.P2Cohesion
-
- getList() - Method in class etomica.atom.iterator.ApiIntraArrayList
-
Returns the list used to generate the pairs.
- getList() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
- getList() - Method in class etomica.molecule.iterator.MpiIntraArrayList
-
Returns the list used to generate the pairs.
- getList() - Method in class org.jmol.script.ScriptVariable
-
- getListeners() - Method in class etomica.integrator.IntegratorEventManager
-
- getListeners() - Method in class etomica.integrator.IntegratorListenerGroupSeries
-
- getLnBias(int) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- getLnBiasDiff() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- getLoad() - Method in class etomica.modules.materialfracture.PotentialCalculationForceStress
-
- getLocale() - Static method in class etomica.graph.view.rasterizer.Messages
-
Implements Localizable.getLocale().
- getLocalVisitor() - Method in class etomica.graph.traversal.AbstractTraversal
-
- getLogAverage(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
-
- getLogAverage(int) - Method in interface etomica.overlap.DataOverlap.DataSourceOverlapLogAvg
-
- getLogAverageAndError(double) - Method in class etomica.overlap.DataOverlap
-
Returns the natural log of the average ratio and its uncertainty for the
given value of alpha
- getLogAverageAndError(boolean, double) - Method in class etomica.overlap.DataOverlap
-
Returns the natural log of the average value from the reference or target
system (as specified) and its uncertainty for the given value of alpha
- getLogError(int) - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
-
- getLogError(int) - Method in interface etomica.overlap.DataOverlap.DataSourceOverlapLogAvg
-
- getLogError(int) - Method in class etomica.overlap.DataOverlap
-
Returns the uncertainty in the log of the average corresponding to the
iAlpha value of alpha.
- getLogLevel() - Static method in class org.jmol.util.Logger
-
- getLowerLimit() - Method in class etomica.models.hexane.SpeciesHexane
-
- getLxy() - Method in class etomica.interfacial.ConfigurationLammps
-
- getMakeLrc() - Method in class etomica.potential.P2SoftSphericalTruncated
-
- getMass() - Method in class etomica.atom.AtomType
-
- getMass() - Method in class etomica.chem.elements.Element
-
- getMass() - Method in class etomica.chem.elements.ElementChemical
-
- getMass() - Method in class etomica.chem.elements.ElementSimple
-
- getMass() - Method in interface etomica.chem.elements.IElement
-
- getMass() - Method in class etomica.potential.P1HardMovingBoundary
-
- getMass(IMolecule) - Method in interface etomica.potential.P2SemiclassicalMolecular.MoleculeInfo
-
Returns the mass of the molecule.
- getMass(IMolecule) - Method in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- getMass() - Method in interface etomica.species.ISpeciesOriented
-
- getMass() - Method in class etomica.species.SpeciesOriented
-
- getMass() - Method in class etomica.species.SpeciesSpheresRotatingMolecule
-
- getMass() - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
-
- getMass() - Method in class etomica.units.systems.LJ
-
- getMassDimension() - Method in class etomica.atom.AtomType
-
- getMassDimension() - Method in class etomica.chem.elements.Element
-
- getMassDimension() - Method in class etomica.potential.P1HardMovingBoundary
-
- getMassDimension() - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
-
- getMathContext() - Method in class etomica.virial.MeterVirialBDBin
-
- getMathContext() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- getMathContext() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- getMatrix() - Method in class org.jmol.util.Quaternion
-
- getMatrixFromFile(String, int) - Method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- getMatrixFromFile(String, int) - Method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- getMaxBlocks() - Method in class etomica.data.AccumulatorAverageCollapsing
-
- getMaxBonds() - Method in class etomica.association.AssociationHelperBranched
-
- getMaxBonds() - Method in class etomica.association.AssociationHelperMolecule
-
- getMaxDistance() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- getMaxDistance() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- getMaxElement() - Method in class etomica.lattice.IndexIteratorTriangular
-
- getMaxElement() - Method in class etomica.lattice.LatticeSum
-
- getMaxElementMin() - Method in class etomica.lattice.IndexIteratorTriangular
-
- getMaxHeight() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getMaximum() - Method in class etomica.graphics.DeviceSlider
-
- getMaximum() - Method in class etomica.graphics.DeviceSpinner
-
- getMaximumFractionDigits() - Method in class etomica.util.ScientificFormat
-
- getMaximumIntegerDigits() - Method in class etomica.util.ScientificFormat
-
- getMaximumSeparation() - Method in class etomica.potential.P2Fene
-
Accessor method for harmonic energy parameter
- getMaximumSeparationDimension() - Method in class etomica.potential.P2Fene
-
- getMaxIterations() - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- getMaxLatticeShell() - Method in class etomica.lattice.LatticeSumCrystal
-
- getMaxLatticeShell() - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- getMaxLatticeShell() - Method in class etomica.normalmode.HarmonicCrystal
-
- getMaxLatticeShell() - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
-
- getMaxLatticeShell() - Method in class etomica.normalmode.NormalModesPotential
-
- getMaxLatticeShell() - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
-
- getMaxLatticeShell() - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
-
- getMaxLatticeShell() - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
- getMaxLatticeShell() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- getMaxNbrsVapor() - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- getMaxPotentialRange() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Returns the maximum range of any potential held by this potential master
- getMaxPotentialRange() - Method in class etomica.nbr.list.PotentialMasterList
-
Returns the maximum range of any potential held by this potential master
- getMaxSleep() - Method in class etomica.graphics.DeviceDelaySlider
-
- getMaxSteps() - Method in class etomica.action.ActionIntegrate
-
Accessor method for the number of doStep calls to be
performed by this integrator after it is started.
- getMaxSteps() - Method in class etomica.action.activity.ActivityIntegrate
-
Accessor method for the number of doStep calls to be
performed by this integrator after it is started.
- getMaxWidth() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getMaxWidth() - Method in class etomica.util.ScientificFormat
-
- getMaxX() - Method in class g3dsys.control.G3DSys
-
- getMaxY() - Method in class g3dsys.control.G3DSys
-
- getMaxZ() - Method in class g3dsys.control.G3DSys
-
- getMCMove() - Method in class etomica.integrator.mcmove.MCMoveEvent
-
- getMCMove() - Method in class etomica.integrator.mcmove.MCMoveTrialCompletedEvent
-
- getMCMove() - Method in class etomica.integrator.mcmove.MCMoveTrialFailedEvent
-
- getMCMove() - Method in class etomica.integrator.mcmove.MCMoveTrialInitiatedEvent
-
- getMCMoveClusterTorsionMulti() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- getMCMoveMoleculeExchange() - Method in class etomica.integrator.IntegratorGEMC
-
Returns the object that performs the molecule-exchange move in the GE
simulation.
- getMCMoves() - Method in class etomica.integrator.mcmove.MCMoveManager
-
Constructs and returns array of all moves added to the integrator.
- getMCMoveVolumeExchange() - Method in class etomica.integrator.IntegratorGEMC
-
Returns the object that performs the volume-exchange move in the GE
simulation.
- getMediaType() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getMembraneDim() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- getMembraneDim() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
The dimension of the membrane (0=x, 1=y, 2=z).
- getMembraneThickness() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
Returns the thickness (angstroms) of each layer of the membrane
(see getNumMembraneLayers)
- getMembraneThicknessPerLayer() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- getMembraneWidth() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- getMembraneWidth() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
Returns the width of the membrane.
- getMessage() - Method in exception etomica.graph.view.rasterizer.SVGConverterException
-
- getMetadata() - Method in interface etomica.graph.model.Edge
-
- getMetadata() - Method in class etomica.graph.model.impl.EdgeImpl
-
- getMetadata() - Method in class etomica.graph.model.impl.NodeImpl
-
- getMetadata() - Method in interface etomica.graph.model.Node
-
- getMeter() - Method in class etomica.graphics.DisplayScrollingGraph
-
Accessor method for the meter that generates the displayed value.
- getMeterPotentialEnergy() - Method in class etomica.integrator.IntegratorBox
-
- getMeterTemperature() - Method in class etomica.integrator.IntegratorMD
-
- getMillerIndex(int) - Method in class etomica.lattice.LatticePlane
-
Returns the current value of the i-th Miller index.
- getMinBondedAtomDistance() - Method in class etomica.association.AssociationHelperBranched
-
- getMinBondedAtomDistance() - Method in class etomica.association.AssociationHelperDouble
-
- getMinBondedMoleculeDistance() - Method in class etomica.association.AssociationHelperMolecule
-
- getMinimum() - Method in class etomica.graphics.DeviceSlider
-
- getMinimum() - Method in class etomica.graphics.DeviceSpinner
-
- getMinimumFractionDigits() - Method in class etomica.util.ScientificFormat
-
- getMinimumIntegerDigits() - Method in class etomica.util.ScientificFormat
-
- getMinNumAtoms() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- getMinRadicalSites() - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
- getMinX() - Method in class g3dsys.control.G3DSys
-
- getMinY() - Method in class g3dsys.control.G3DSys
-
- getMinZ() - Method in class g3dsys.control.G3DSys
-
- getMobileSpecies() - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
- getModelSelectedSpecies() - Method in class etomica.virial.GUI.models.AppModelMixtureBuilder
-
- getModelSpeciesSelection() - Method in class etomica.virial.GUI.models.AppModelMixtureBuilder
-
- getModeNum() - Method in class etomica.normalmode.MCMoveHarmonic
-
- getModeSigns() - Method in class etomica.action.CalcVibrationalModes
-
Returns a one dimensional array of length 3 with the total number of
positive, negative, and imaginary modes.
- getModifier() - Method in class etomica.action.ActionToggle
-
Returns the boolean modifier used by this action.
- getModifier() - Method in class etomica.graphics.DeviceBox
-
Accessor method for the modifier that receives the edit.
- getModifier() - Method in class etomica.graphics.DeviceCheckBox
-
Specifies the boolean modifier that is set between true and false by the button.
- getModifier() - Method in class etomica.graphics.DeviceSlider
-
- getModifier() - Method in class etomica.graphics.DeviceSpinner
-
- getModifier() - Method in class etomica.graphics.DeviceThermoSlider
-
- getModifier() - Method in class etomica.graphics.DeviceToggleRadioButtons
-
Specifies the boolean modifier that is set between true and false by the button.
- getModifier() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- getModifier() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
- getModifier() - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
- getMolecularModelDisplayName() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getMolecularModelDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getMolecule() - Method in class etomica.association.MoleculeSourceRandomDimer
-
- getMolecule() - Method in class etomica.association.MoleculeSourceRandomMonomer
-
- getMolecule(int) - Method in class etomica.box.AtomSetAllMolecules
-
- getMolecule() - Method in class etomica.box.BoxMoleculeEvent
-
- getMolecule(int) - Method in interface etomica.molecule.IMoleculeList
-
Returns the i-th atom, with numbering beginning from 0.
- getMolecule() - Method in class etomica.molecule.iterator.MoleculeIteratorSinglet
-
- getMolecule(int) - Method in class etomica.molecule.MoleculeArrayList
-
- getMolecule(int) - Method in class etomica.molecule.MoleculeListWrapper
-
Part of implementation of AtomSet interface.
- getMolecule(int) - Method in class etomica.molecule.MoleculePair
-
- getMolecule(int) - Method in class etomica.molecule.MoleculesetArray
-
Part of implementation of AtomSet interface.
- getMolecule(int) - Method in class etomica.molecule.MoleculeSetSinglet
-
- getMolecule() - Method in interface etomica.molecule.MoleculeSource
-
Returns an atom.
- getMolecule() - Method in class etomica.molecule.MoleculeSourceRandomMolecule
-
returns a random molecule from the box
- getMoleculeCount() - Method in class etomica.box.AtomSetAllMolecules
-
- getMoleculeCount() - Method in interface etomica.molecule.IMoleculeList
-
- getMoleculeCount() - Method in class etomica.molecule.MoleculeArrayList
-
- getMoleculeCount() - Method in class etomica.molecule.MoleculeListWrapper
-
Returns the length of the wrapped array.
- getMoleculeCount() - Method in class etomica.molecule.MoleculePair
-
- getMoleculeCount() - Method in class etomica.molecule.MoleculesetArray
-
Returns the length of the wrapped array.
- getMoleculeCount() - Method in class etomica.molecule.MoleculeSetSinglet
-
- getMoleculeDataInfo() - Method in interface etomica.data.DataSourceMolecular
-
- getMoleculeDataInfo() - Method in class etomica.data.meter.MeterNMolecules
-
- getMoleculeDataInfo() - Method in class etomica.modules.interfacial.MeterOrientation
-
- getMoleculeDisplayName() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getMoleculeDisplayName() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getMoleculeList(ISpecies) - Method in class etomica.box.Box
-
Returns the list of molecules of the given species.
- getMoleculeList() - Method in class etomica.box.Box
-
- getMoleculeList(IMolecule) - Method in interface etomica.molecule.MoleculeToMoleculeList
-
Returns the ArrayList that this instance associates with the given atom.
- getMoleculeList(IMolecule) - Method in class etomica.molecule.MoleculeToMoleculeListSpecies
-
- getMoleculeList(IMolecule) - Method in class etomica.molecule.MoleculeToMoleculeSetFixed
-
- getMoleculeListDisplayLSM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getMoleculeListDisplayLSM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getMoleculeListDisplayString() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getMoleculeListDisplayTable() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getMoleculeListDisplayTable() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getMoleculeListDisplayTM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getMoleculeListDisplayTM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getMoleculeListDisplayTMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getMoleculeListDisplayTMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getMoleculeOffset() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- getMoleculeOffset() - Method in class etomica.modules.sam.ConfigurationSAM
-
- getMoleculeOrientation(IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- getMoleculeOrientation(IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- getMoleculeOrientation(IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
-
return the initial Orientation of the molecule
- getMolecules() - Method in class etomica.parser.ParmedStructure
-
Gets the list of all molecules in the Structure, initialized with their coordinates in space.
- getMolecules(Box) - Static method in class etomica.util.Debug
-
Returns an AtomPair containing the two atoms with global indices
ATOM1_INDEX and ATOM2_INDEX within the given box.
- getMoleculeSource() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
Returns the AtomSource this class uses to pick molecules to delete.
- getMoleculeSource() - Method in class etomica.models.hexane.MCMoveCBMC
-
Returns the AtomSource used to select Atoms acted on by MC trials.
- getMoment() - Method in class etomica.modules.vle.VLESim
-
- getMoment(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getMoment(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getMoment(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getMomentAndAxes(IAtomOriented) - Method in interface etomica.potential.P2SemiclassicalAtomic.AtomInfo
-
Returns the moment of inertia as a vector containing Ix, Iy, Iz and also the principle axes.
- getMomentAndAxes(IMolecule) - Method in interface etomica.potential.P2SemiclassicalMolecular.MoleculeInfo
-
Returns the moment of inertia as a vector containing Ix, Iy, Iz
and also the principle axes.
- getMomentAndAxes(IMolecule) - Method in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- getMomentOfInertia() - Method in class etomica.atom.AtomTypeOriented
-
Returns the principal components of the moment of inertia of the
atom within the body-fixed frame.
- getMomentOfInertia() - Method in interface etomica.species.ISpeciesOriented
-
Returns the principle components of the moment of inertia of the
molecule within the body-fixed frame.
- getMomentOfInertia() - Method in class etomica.species.SpeciesOriented
-
- getMomentOfInertia() - Method in class etomica.species.SpeciesSpheresRotatingMolecule
-
- getMomentSquare(int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getMonomerColor() - Method in class etomica.association.ColorSchemeSmer
-
Returns the color used for all dimers.
- getMove() - Method in class etomica.data.DataSourceAcceptanceRatio
-
- getMoveEventManager() - Method in class etomica.integrator.IntegratorManagerMC
-
- getMoveEventManager() - Method in class etomica.integrator.IntegratorMC
-
- getMoveManager() - Method in class etomica.integrator.IntegratorManagerMC
-
- getMoveManager() - Method in class etomica.integrator.IntegratorMC
-
- getMSMCGraphs(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- getMSMCGraphs(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- getMSMCGraphs(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- getMSMCGraphs(boolean, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- getMSMCGraphs(boolean, int, int[]) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- getMSMCGraphs(boolean, int) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- getMSMCGraphs(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- getMSMCGraphs(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- getMSMCGraphsEX(boolean) - Method in class etomica.virial.cluster.ExternalVirialDiagrams
-
- getMType() - Method in class etomica.models.water.SpeciesWater4P
-
- getMType() - Method in class etomica.models.water.SpeciesWater4PCOM
-
- getMType() - Method in class etomica.models.water.SpeciesWater4POriented
-
- getMu() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
Accessor method for the chemical potential of th insertion/deletion species.
- getMuDimension() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
Indicates that chemical potential has dimensions of energy.
- getMultiBDcount() - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- getMultiBDfrac() - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- getMultiBonds() - Method in class etomica.virial.ClusterBondsNonAdditive
-
Returns the list of multiBonds to multiply.
- getMulticount() - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- getN() - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- getN() - Method in class etomica.potential.P4TorsionDreiding
-
- getn() - Method in class etomica.virial.ClusterWheatleyPartitionScreening.FrequencyCounter
-
- getN1() - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getN1(byte) - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getN1() - Method in class etomica.graph.isomorphism.NodePair
-
- getN2() - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getN2(byte) - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- getN2() - Method in class etomica.graph.isomorphism.NodePair
-
- getName() - Method in class etomica.data.meter.MeterDihedralAngle
-
- getName() - Method in class etomica.data.meter.MeterMomentumCOM
-
- getName() - Method in class etomica.data.meter.MeterPositionCOM
-
- getName() - Method in class etomica.data.meter.MeterPressureHardTensor
-
- getName() - Method in class etomica.data.meter.MeterRDF
-
- getName() - Method in class etomica.data.meter.MeterRDFPC
-
- getName() - Method in class etomica.data.meter.MeterTensorVelocity
-
- getName() - Method in class etomica.graph.engine.impl.PropertyImpl
-
- getName() - Method in class etomica.graph.engine.impl.VariableImpl
-
- getName() - Method in interface etomica.graph.engine.Parser.Property
-
- getName() - Method in interface etomica.graph.engine.Parser.Variable
-
- getName() - Method in class etomica.graph.view.rasterizer.SVGConverterDocumentSource
-
- getName() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
-
- getName() - Method in interface etomica.graph.view.rasterizer.SVGConverterSource
-
Returns the name of the source.
- getName() - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
-
- getName() - Method in class etomica.graphics.EtomicaTheme
-
- getName() - Method in class etomica.mappedRdf.MeterMappedRdf
-
- getName() - Method in class etomica.meta.properties.ArrayProperty
-
- getName() - Method in class etomica.meta.properties.AtomListProperty
-
- getName() - Method in class etomica.meta.properties.InstanceProperty
-
- getName() - Method in class etomica.meta.properties.MoleculeListProperty
-
- getName() - Method in interface etomica.meta.properties.Property
-
- getName() - Method in class etomica.meta.properties.VectorProperty
-
- getName() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- getName() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- getName() - Method in class etomica.normalmode.MeterNormalMode
-
- getName() - Method in class etomica.server.EtomicaServer
-
- getName() - Method in enum org.jmol.constant.EnumStereoMode
-
- getNaturalIsotope(int) - Static method in class org.jmol.util.Elements
-
- getNBennetPoints() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- getNBennetPoints() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- getNBins() - Method in class etomica.data.AccumulatorHistogram
-
- getNBins() - Method in interface etomica.data.histogram.Histogram
-
Returns the number of bins in the histogram.
- getNBins() - Method in class etomica.data.histogram.HistogramDiscrete
-
- getNBins() - Method in class etomica.data.histogram.HistogramNotSoSimple
-
- getNBins() - Method in class etomica.data.histogram.HistogramReweightedData
-
- getNBins() - Method in class etomica.data.histogram.HistogramSimple
-
- getNbrAtoms(Box) - Method in class etomica.normalmode.P1ConstraintNbr
-
- getNbrCellIterator() - Method in class etomica.nbr.cell.Api1ACell
-
- getNbrCellIterator() - Method in class etomica.nbr.cell.ApiAACell
-
- getNbrCellIterator() - Method in interface etomica.nbr.cell.AtomsetIteratorCellular
-
- getNbrCellIterator() - Method in interface etomica.nbr.cell.molecule.MoleculesetIteratorCellular
-
- getNbrCellIterator() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
- getNbrCellIterator() - Method in class etomica.nbr.cell.molecule.MpiAACell
-
- getNbrCellManager(Box) - Method in class etomica.nbr.cell.PotentialMasterCell
-
- getNbrCellManager(Box) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- getNbrCellManager(Box) - Method in class etomica.nbr.list.PotentialMasterList
-
- getNbrCellManager(Box) - Method in class etomica.nbr.PotentialMasterHybrid
-
- getNbrCellManagerThreaded(Box) - Method in class etomica.threaded.domain.PotentialMasterListThreaded
-
- getNbrDistance() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- getNCellModifier() - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
- getNCellNum() - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
- getNCellNum() - Method in class etomica.normalmode.NormalModes3D
-
- getNCells() - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- getNCells() - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- getNCellsX() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- getNCellsX() - Method in class etomica.modules.sam.ConfigurationSAM
-
- getNCellsZ() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- getNCellsZ() - Method in class etomica.modules.sam.ConfigurationSAM
-
- getNCrossLinkersAcid() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- getNData() - Method in class etomica.data.types.DataGroup
-
Returns the number of data objects encapsulated by this DataGroup.
- getNDataInfo() - Method in class etomica.data.types.DataGroup.DataInfoGroup
-
- getNDiAcid() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- getNDiagrams() - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- getNDiol() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- getNegativePrefix() - Method in class etomica.util.ScientificFormat
-
- getNegativeSuffix() - Method in class etomica.util.ScientificFormat
-
- getNeighborCriteria() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- getNeighborCriteria() - Method in class etomica.nbr.list.PotentialMasterList
-
- getNeighborDistance() - Method in class etomica.lattice.CellLattice.NeighborIterator
-
- getNeighborManager(Box) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- getNeighborManager(Box) - Method in class etomica.nbr.list.PotentialMasterList
-
- getNeighborManager(Box) - Method in class etomica.nbr.PotentialMasterHybrid
-
- getNeighborRange() - Method in class etomica.nbr.CriterionPositionWall
-
- getNeighborRange() - Method in class etomica.nbr.CriterionSimple
-
- getNeighborRange() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- getNeighborRangeDimension() - Method in class etomica.nbr.CriterionPositionWall
-
- getNeighborRangeDimension() - Method in class etomica.nbr.CriterionSimple
-
- getNeighborRangeDimension() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- getNeighborVertexesArrays() - Static method in class org.jmol.util.Geodesic
-
- getNewId() - Method in class etomica.meta.SimulationModel
-
- getNewPartners() - Method in class etomica.potential.PotentialReactive.BondChangeData
-
- getNewValue() - Method in class etomica.server.representations.PropertyUpdate
-
- getNGraft() - Method in class etomica.modules.colloid.ConfigurationColloid
-
- getNInsert() - Method in class etomica.data.meter.MeterWidomInsertion
-
Accessor to number of Widom insertions attempted with each call to
currentValue
- getNInsert() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
Accessor to number of Widom insertions attempted with each call to
currentValue
- getNInsert() - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Accessor to number of Widom insertions attempted with each call to
currentValue
- getNitrogenType() - Method in class etomica.models.nitrogen.SpeciesN2
-
- getNitrogenType() - Method in class etomica.models.nitrogen.SpeciesN2B
-
- getNitrogenType() - Method in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- getNMajor() - Method in class etomica.graphics.DeviceSlider
-
- getNMinor() - Method in class etomica.graphics.DeviceSlider
-
- getNMolecules(ISpecies) - Method in class etomica.box.Box
-
- getNMonoAcid() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- getNMonoOl() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- getNode(byte) - Method in interface etomica.graph.model.Graph
-
- getNode(byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- getNoisyAdjustment() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
- getNominalFluctuation() - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- getNominalFrequency() - Method in class etomica.integrator.mcmove.MCMove
-
Returns a nominal, unnormalized frequency for performing this move,
relative to the other moves that have been added to the integrator.
- getNonBondedInteractionModel() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getNonBondedInteractionModel() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getNoneCliqueCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getNoneCliques() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getNonPolarizationEnergy(IMoleculeList) - Method in class etomica.models.co2.PNCO2GCPM
-
This returns the pairwise-additive portion of the GCPM potential for a
pair of atoms (dispersion + fixed-charge electrostatics)
- getNonPolarizationEnergy(IMoleculeList) - Method in class etomica.models.co2.PNGCPM
-
This returns the pairwise-additive portion of the GCPM potential for a
pair of atoms (dispersion + fixed-charge electrostatics)
- getNonPolarizationEnergy(IMoleculeList) - Method in class etomica.models.water.PNWaterGCPM
-
This returns the pairwise-additive portion of the GCPM potential for a
pair of atoms (dispersion + fixed-charge electrostatics)
- getNoOfSpheres() - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- getNoOfSteps() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- getNoOfSteps() - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
-
- getNoOfStepsField() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- getNorm() - Method in class etomica.math.Quaternion
-
Returns the norm of the Quaternion q defined as N = sqrt(q*q)
- getNormal(Vector) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
-
Returns a unit normal to the argument vector
- getNormal() - Method in class org.jmol.util.Quaternion
-
- getNormalDirected(Vector3f) - Method in class org.jmol.util.Quaternion
-
- getNormalFromCenter(Point3f, Point3f, Point3f, Point3f, boolean, Vector3f) - Static method in class org.jmol.util.Measure
-
- getNormalModes() - Method in class etomica.normalmode.HarmonicCrystal
-
- getNormalModes() - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
-
- getNormalModes() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- getNormalModes() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- getNormalThroughPoints(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- getNormalToLine(Point3f, Point3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- getNormixCount() - Static method in class org.jmol.util.Normix
-
- getNormixV(Vector3f, BitSet) - Static method in class org.jmol.util.Normix
-
- getnPoints() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- getnReactCO() - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- getNRows() - Method in class etomica.data.types.DataTable.DataInfoTable
-
Returns the number of rows in the table
- getNRows() - Method in class etomica.data.types.DataTable.DataInfoTableFactory
-
Returns the number of rows.
- getNRows() - Method in class etomica.data.types.DataTable
-
Returns the number of rows in each and every column of the table.
- getNSpheres() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getNSpheres() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getNthSpeciesAdded() - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- getNthSpeciesSelectedIndex() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getNTicks() - Method in class etomica.graphics.DisplayScrollingGraph
-
- getNType() - Method in class etomica.paracetamol.SpeciesParacetamol
-
- getNullPotential(AtomType) - Method in class etomica.integrator.IntegratorHard
-
- getNumAlpha() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- getNumAlpha() - Method in interface etomica.overlap.AlphaSource
-
Returns the number of possible alpha values.
- getNumAlpha() - Method in class etomica.overlap.MeterOverlap
-
- getNumAlpha() - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- getNumAlpha() - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
Returns the number of alpha values used for the production stage of the
simulation
- getNumAlpha() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
Returns the number of alpha values used for the production stage of the
simulation
- getNumAtoms() - Method in class etomica.chem.models.ModelChain
-
Returns the number of atoms per chain molecule.
- getNumAtoms() - Method in class etomica.zeolite.ConfigurationFileXYZ
-
- getNumBeads() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- getNumber() - Method in class etomica.modules.materialfracture.StrainColorScheme
-
- getNumberFraction() - Method in class etomica.species.SpeciesSpheresHetero
-
Returns the number fraction of each child type created by this factory.
- getNumberOfTrials() - Method in class etomica.models.hexane.MCMoveCBMC
-
- getNumCO() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- getNumCollapseBins() - Method in class etomica.data.history.HistoryCollapsing
-
- getNumConnections() - Method in class etomica.virial.cluster.ClusterDiagram
-
returns the number of active connections in the cluster.
- getNumDataSinks() - Method in class etomica.data.DataDistributer
-
- getNumDataSinks() - Method in class etomica.data.DataGroupSplitter
-
- getNumDataSinks() - Method in class etomica.data.DataSplitter
-
- getNumDataSinks() - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
-
- getNumDataSinks() - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsingSplit
-
- getNumDelete() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- getNumDigitColumns() - Method in class etomica.graphics.DisplayTable
-
- getNumEquilibrationSubsteps() - Method in class etomica.thermointegration.IntegratorThermodynamic
-
Returns the number of steps equilibration steps performed at each
thermodynamic state point before data collection begins.
- getNumerator() - Method in interface etomica.graph.model.Coefficient
-
- getNumerator() - Method in class etomica.graph.model.impl.CoefficientImpl
-
- getNumFieldPoints() - Method in class etomica.graph.operations.Mul.MulParameters
-
- getNumInsert() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- getNumLeafAtoms() - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- getNumLeafAtoms() - Method in class etomica.AlkaneEH.SpeciesMethane
-
- getNumLeafAtoms() - Method in class etomica.models.nitrogen.SpeciesN2
-
- getNumLeafAtoms() - Method in class etomica.models.nitrogen.SpeciesN2B
-
- getNumLeafAtoms() - Method in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- getNumLeafAtoms() - Method in class etomica.models.OPLS.SpeciesAceticAcid
-
- getNumLeafAtoms() - Method in class etomica.models.rowley.SpeciesEthanol
-
- getNumLeafAtoms() - Method in class etomica.models.rowley.SpeciesMethanol
-
- getNumLeafAtoms() - Method in class etomica.models.traPPE.SpeciesMethanol
-
- getNumLeafAtoms() - Method in class etomica.models.water.SpeciesWater3P
-
- getNumLeafAtoms() - Method in class etomica.models.water.SpeciesWater3POriented
-
- getNumLeafAtoms() - Method in class etomica.models.water.SpeciesWater4P
-
- getNumLeafAtoms() - Method in class etomica.models.water.SpeciesWater4PCOM
-
- getNumLeafAtoms() - Method in class etomica.models.water.SpeciesWater4POriented
-
- getNumLeafAtoms() - Method in class etomica.normalmode.SpeciesHSDimer
-
- getNumLeafAtoms() - Method in class etomica.paracetamol.SpeciesParacetamol
-
- getNumLeafAtoms() - Method in class etomica.species.SpeciesSpheres
-
- getNumLeafAtoms() - Method in class etomica.species.SpeciesSpheresCustom
-
- getNumLeafAtoms() - Method in class etomica.species.SpeciesSpheresHetero
-
- getNumLeafAtoms() - Method in class etomica.species.SpeciesSpheresMono
-
- getNumLeafAtoms() - Method in class etomica.virial.Species7SiteRigidSF6
-
- getNumLeafAtoms() - Method in class etomica.virial.SpeciesAnthracene3site464
-
- getNumLeafAtoms() - Method in class etomica.virial.SpeciesAnthracene3site545
-
- getNumLeafAtoms() - Method in class etomica.virial.SpeciesMethane
-
- getNumLeafAtoms() - Method in class etomica.virial.SpeciesPh3site464
-
- getNumLeafAtoms() - Method in class etomica.virial.SpeciesPh3site545
-
- getNumLeafAtoms() - Method in class etomica.virial.SpeciesTraPPEAnthracene
-
- getNumLeafAtoms() - Method in class etomica.virial.SpeciesTraPPECO2
-
- getNumLeafAtoms() - Method in class etomica.virial.SpeciesTraPPENaphthalene
-
- getNumLeafAtoms() - Method in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- getNumMembraneLayers() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- getNumMembraneLayers() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
Returns the number of membrane layers.
- getNumNodes() - Method in class etomica.virial.cluster.ClusterCollapsedTreeNode
-
- getNumNodes() - Method in class etomica.virial.cluster.ClusterTreeNode
-
- getNumO2() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- getNumRawData() - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getNumRawData() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getNumRootPoints() - Method in class etomica.virial.cluster.ClusterDiagram
-
- getNumSubSteps() - Method in class etomica.overlap.IntegratorOverlap
-
Retruns the number of total number of integrator steps the sub-integrators
perform for every step of the overlap integrator.
- getNumSubsteps() - Method in class etomica.thermointegration.IntegratorThermodynamic
-
Returns the number of steps performed at each thermodynamic state point.
- getNumSubSteps() - Method in class etomica.virial.overlap.IntegratorOverlap
-
Retruns the number of total number of integrator steps the sub-integrators
perform for every step of the overlap integrator.
- getNumSurfaceSites() - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- getNumSurfaceSites() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- getNumTargets() - Method in class etomica.virial.overlap.DataVirialOverlap
-
- getNumTrial() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- getNumTrial() - Method in class etomica.virial.MCMoveClusterRingRegrow
-
- getNumTrial() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- getNumUpdates() - Method in class etomica.nbr.list.NeighborListManager
-
Returns the number of times the neighbor lists have been updated.
- getNumValues() - Method in class etomica.virial.ClusterSumIC
-
- getNumXCells() - Method in class etomica.modules.sam.Sam
-
- getNumZCells() - Method in class etomica.modules.sam.Sam
-
- getNValues() - Method in class etomica.data.DataSourceUniform
-
Accessor method for number of values.
- getObject() - Method in class etomica.modifier.ModifierGeneral
-
- getObject(int) - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
-
- getOctant(Point3f) - Static method in class org.jmol.util.Quadric
-
- getOelement() - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- getOffset() - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- getOffset() - Method in class etomica.modules.sam.P1Sinusoidal
-
- getOldPartners() - Method in class etomica.potential.PotentialReactive.BondChangeData
-
- getOmegaSquared() - Method in interface etomica.normalmode.NormalModes
-
Returns an array giving the frequencies (squared) corresponding to the normal-mode
motions.
- getOmegaSquared() - Method in class etomica.normalmode.NormalModes1DHR
-
- getOmegaSquared() - Method in class etomica.normalmode.NormalModes2D
-
- getOmegaSquared() - Method in class etomica.normalmode.NormalModes3D
-
- getOmegaSquared() - Method in class etomica.normalmode.NormalModesFromFile
-
- getOmegaSquared() - Method in class etomica.normalmode.NormalModesMolecular
-
- getOmegaSquared() - Method in class etomica.normalmode.NormalModesPotential
-
- getOmegaSquared() - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- getOmegaSquared() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- getOneEValButtonsVisibility() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
- getOneWVButtonsVisibility() - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
- getOperation() - Method in class etomica.graph.engine.impl.BinaryOpImpl
-
- getOperation() - Method in class etomica.graph.engine.impl.UnaryOpImpl
-
- getOperation() - Method in interface etomica.graph.engine.Parser.BinaryOp
-
- getOperation() - Method in interface etomica.graph.engine.Parser.UnaryOp
-
- getOptionDescription() - Method in interface etomica.graph.view.rasterizer.Main.OptionHandler
-
Returns the description for this option
- getOptionValuesLength() - Method in class etomica.graph.view.rasterizer.Main.NoValueOptionHandler
-
- getOptionValuesLength() - Method in interface etomica.graph.view.rasterizer.Main.OptionHandler
-
Returns the number of values which the option handler requires.
- getOptionValuesLength() - Method in class etomica.graph.view.rasterizer.Main.SingleValueOptionHandler
-
- getOrderBeta() - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- getOrientation() - Method in class etomica.atom.AtomOriented
-
- getOrientation() - Method in class etomica.atom.AtomOrientedDynamic
-
- getOrientation() - Method in interface etomica.atom.IAtomOriented
-
Returns the orientation of the IAtom.
- getOrientation() - Method in class etomica.math.Quaternion
-
Returns an orientation corresponding to the rotation of cartesian coordinate frame {i,j,k}
by the axis and angle associated with the Quaternion q.
- getOrientation() - Method in interface etomica.molecule.IMoleculeOriented
-
Returns the orientation of the IAtom.
- getOrientation() - Method in class etomica.molecule.MoleculeOriented
-
- getOrientationIndex(Vector) - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- getOrientationIndex(Vector) - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- getOrigin() - Method in class etomica.graphics.DisplayBox
-
- getOrigin() - Method in class etomica.graphics.DisplayPolytope
-
- getOrigin() - Method in class etomica.lattice.LatticePlane
-
- getOtherAngles() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- getOtherDensities() - Method in class etomica.normalmode.MeterDDP
-
- getOtherDensities() - Method in class etomica.normalmode.MeterDP
-
- getOtherTemperature() - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- getOtherTemperatures() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- getOtherTemperatures() - Method in class etomica.normalmode.MeterTargetTP
-
- getOType() - Method in class etomica.models.traPPE.SpeciesMethanol
-
- getOType() - Method in class etomica.paracetamol.SpeciesParacetamol
-
- getOut() - Method in class etomica.data.DataSinkConsole
-
Method called to express incredulity.
- getOutDegree(byte) - Method in interface etomica.graph.model.Graph
-
- getOutDegree(byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- getOutDegree() - Method in class etomica.virial.ClusterSumHS
-
Returns outDegee (number of bonds for each point) of the configuration
passed to checkConfig
- getOutDegree() - Method in interface etomica.virial.ClusterWheatley
-
Returns outDegee (number of bonds for each point) of the configuration
passed to checkConfig
- getOutDegree() - Method in class etomica.virial.ClusterWheatleyHS
-
Returns outDegee (number of bonds for each point) of the configuration
passed to checkConfig
- getOutDegree() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
Returns outDegee (number of bonds for each point) of the configuration
passed to checkConfig
- getOutDegreeCore() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getOutDegreeWell() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getOuterGraph() - Method in class etomica.graph.iterators.CartesianIterator
-
- getOuterIterator() - Method in class etomica.atom.iterator.ApiInnerVariable
-
Accessor method for the outer-loop atom iterator.
- getOuterIterator() - Method in class etomica.atom.iterator.ApiIntergroup
-
Accessor method for the outer-loop atom iterator.
- getOuterIterator() - Method in class etomica.graph.iterators.CartesianIterator
-
- getOuterIterator() - Method in class etomica.molecule.iterator.MpiInnerFixed
-
Accessor method for the outer-loop atom iterator.
- getOuterIterator() - Method in class etomica.molecule.iterator.MpiInnerVariable
-
Accessor method for the outer-loop atom iterator.
- getOuterList() - Method in class etomica.atom.iterator.ApiInterArrayList
-
Returns the outer list used to generate the pairs.
- getOuterList() - Method in class etomica.molecule.iterator.MpiInterArrayList
-
Returns the outer list used to generate the pairs.
- getOuterPermutation() - Method in class etomica.graph.iterators.CartesianPermutator
-
- getOuterPermutator() - Method in class etomica.graph.iterators.CartesianPermutator
-
- getOuterRadius() - Method in class etomica.atom.AtomTypeSpheroPolyhedron
-
- getOutNode(byte, byte) - Method in interface etomica.graph.model.Graph
-
- getOutNode(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- getOverlapAverage() - Method in class etomica.virial.overlap.DataVirialOverlap
-
Returns the ratio of the reference to target overlap-to-virial ratios
(which reduces to reference/target) for the optimal value of the Bennett
parameter.
- getOverlapAverage(int) - Method in class etomica.virial.overlap.DataVirialOverlap
-
Returns the ratio of the reference to target overlap-to-virial ratios
(which reduces to target/reference) for the given value of the Bennet
parameter.
- getOverlapAverageAndError() - Method in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
-
- getOverlapAverageAndError() - Method in class etomica.overlap.DataOverlap
-
Returns the ratio of the reference to target overlap-to-virial ratios
(which reduces to reference/target) for the optimal value of the Bennett
parameter.
- getOverlapAverageAndError() - Method in class etomica.virial.overlap.DataSourceVirialOverlap
-
Returns the ratio of the reference to target overlap-to-virial ratios
(which reduces to reference/target) for the optimal value of the Bennett
parameter.
- getOverlapAverageAndErrorForAlpha(double) - Method in class etomica.virial.overlap.DataVirialOverlap
-
Returns the overlap average and uncertainty for a given value of alpha.
- getOverlapAverageForAlpha(double) - Method in class etomica.virial.overlap.DataSourceVirialOverlap
-
- getOxygenType() - Method in class etomica.models.rowley.SpeciesEthanol
-
- getOxygenType() - Method in class etomica.models.rowley.SpeciesMethanol
-
- getOxygenType() - Method in class etomica.models.water.SpeciesWater3P
-
- getOxygenType() - Method in class etomica.models.water.SpeciesWater3POriented
-
- getOxygenType() - Method in class etomica.models.water.SpeciesWater4P
-
- getOxygenType() - Method in class etomica.models.water.SpeciesWater4PCOM
-
- getOxygenType() - Method in class etomica.models.water.SpeciesWater4POriented
-
- getOxygenType() - Method in class etomica.virial.SpeciesTraPPECO2
-
- getP(int) - Method in class etomica.normalmode.MeterDDP
-
- getP(int) - Method in class etomica.normalmode.MeterDP
-
- getp1Counter() - Method in class etomica.normalmode.P1ConstraintNbrHcp
-
- getPaddingSigma() - Method in class etomica.graphics.DisplayBox
-
Returns the amount of padding added around the edge of the drawing area.
- getPaintAction(Box) - Method in class etomica.graphics.SimulationGraphic
-
getPaintAction()
- getPairAgent(AtomType, AtomType) - Method in class etomica.models.co2.PNGCPM
-
- getPairAgent(AtomType, AtomType) - Method in class etomica.models.co2.PNGCPMX
-
- getPairMoleculesIndex(IMolecule, IMolecule, boolean) - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- getPairMoleculesIndex(IMolecule, IMolecule, boolean) - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- getPairSiteValidation(String, IMolecularModel_SpeciesFactory[]) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- getPalette(String) - Static method in enum org.jmol.constant.EnumPalette
-
- getPaletteID(String) - Static method in enum org.jmol.constant.EnumPalette
-
- getPaletteName(byte) - Static method in enum org.jmol.constant.EnumPalette
-
- getPanel() - Method in class etomica.graphics.DeviceSlider
-
- getPanel() - Method in class etomica.graphics.DeviceSpinner
-
- getPanel() - Method in class etomica.graphics.SimulationGraphic
-
A visual display of the simulation via a JPanel.
- getPanel() - Method in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- getPanel() - Method in class etomica.modules.crystalviewer.LatticeEditor
-
- getParallelAxis(IMolecule) - Method in class etomica.models.co2.PNGCPM.GCPMAgent
-
- getParamAndValues() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getParamAndValues() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getParameter(double) - Method in class etomica.models.nitrogen.BetaPhaseLatticeParameter
-
- getParameter(double) - Method in class etomica.models.nitrogen.BetaPhaseLatticeParameterLS
-
- getParameter(int) - Method in class etomica.models.nitrogen.BetaPhaseLatticeParameterNA
-
- getParameterCount() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getParameterCount() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getParameters() - Static method in class etomica.modules.render.RenderMD
-
- getParameters() - Static method in class etomica.simulation.prototypes.HSMD3D
-
- getParametersArray() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getParametersArray() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getParameterValue(String) - Method in class etomica.graphics.DevicePlotPoints
-
Returns the value of the function parameter slider.
- getParameterWrapper() - Method in class etomica.util.ParseArgs
-
Returns the parameter wrapper.
- getParameterWrapper() - Method in class etomica.util.ReadParameters
-
Returns the parameter wrapper.
- getParameterWrapper() - Method in class etomica.util.WriteParameters
-
Returns the parameter wrapper.
- getParamType(int) - Static method in class org.jmol.script.Token
-
- getParentGroup() - Method in class etomica.atom.Atom
-
- getParentGroup() - Method in interface etomica.atom.IAtom
-
- getParsers() - Method in class etomica.util.ParameterBase
-
- getPartner(int) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- getPbcEnforcer() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- getPbcEnforcer() - Method in class etomica.nbr.list.NeighborListManager
-
- getPCenter(int) - Method in class etomica.normalmode.MeterDDP
-
- getPCenter(int) - Method in class etomica.normalmode.MeterDP
-
- getPdbBondInfo(int) - Static method in class org.jmol.viewer.JmolConstants
-
- getPendingActions() - Method in interface etomica.action.activity.ActivityGroup
-
Returns all actions from this group that have not yet started.
- getPendingActions() - Method in class etomica.action.activity.ActivityGroupParallel
-
- getPendingActions() - Method in class etomica.action.activity.ActivityGroupSeries
-
- getPerimeter() - Method in class etomica.math.geometry.Cube
-
Returns 12*edgeLength
- getPerimeter() - Method in class etomica.math.geometry.Cuboid
-
- getPerimeter() - Method in class etomica.math.geometry.Parallelepiped
-
- getPerimeter() - Method in class etomica.math.geometry.Parallelogram
-
- getPerimeter() - Method in class etomica.math.geometry.Polygon
-
Returns the sum of the length of the edges of the polygon
- getPerimeter() - Method in class etomica.math.geometry.Polyhedron
-
Returns the sum of the length of the edges of the polyhedron
- getPerimeter() - Method in class etomica.math.geometry.Rectangle
-
Returns the perimeter of the rectangle.
- getPeriodicity(int) - Method in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
-
- getPeriodicity(int) - Method in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
-
- getPeriodicity(int) - Method in class etomica.space.Boundary
-
Returns true if the boundary is periodic in the given direction (as
defined by the getEdgeVector method).
- getPeriodicity(int) - Method in class etomica.space.BoundaryDeformablePeriodic
-
- getPeriodicity(int) - Method in class etomica.space.BoundaryRectangularNonperiodic
-
- getPeriodicity(int) - Method in class etomica.space.BoundaryRectangularPeriodic
-
- getPeriodicity(int) - Method in class etomica.space.BoundaryRectangularPore
-
- getPeriodicity(int) - Method in class etomica.space.BoundaryRectangularSlit
-
- getPeriodicity(int) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
-
- getPerp(Vector, Vector, Vector) - Method in class etomica.models.co2.P2CO2H2OWheatley
-
- getPerp(Vector, Vector, Vector) - Method in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- getPerp(Vector, Vector, Vector) - Method in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- getPerspectiveDepth() - Method in class g3dsys.control.G3DSys
-
- getPhaseAngles() - Method in class etomica.normalmode.NormalModesVariable
-
- getPhi() - Method in class etomica.potential.P4TorsionDreiding
-
- getPhongExponent() - Static method in class org.jmol.util.GData
-
- getPickedDiagram() - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- getPickedDiagram() - Method in interface etomica.virial.cluster.DiagramSource
-
- getPixelDepth() - Method in class g3dsys.control.G3DSys
-
Gets the pixel depth of the display (zbuffer)
- getPixelHeight() - Method in class g3dsys.control.G3DSys
-
Gets the pixel height of the display
- getPixelUnit() - Method in class etomica.graphics.DisplayBox
-
- getPixelUnit() - Method in class etomica.graphics.DisplayCanvas
-
Returns unit for conversion between simulation units and display pixels.
- getPixelUnit() - Method in class etomica.graphics.DisplayPolytope
-
Returns unit for conversion between simulation units and display pixels.
- getPixelUnitToMillimeter() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getPixelWidth() - Method in class g3dsys.control.G3DSys
-
Gets the pixel width of the display
- getPlane() - Method in class etomica.lattice.LatticePlane
-
- getPlaneColor() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Gets the color of the plane.
- getPlaneProjection(Point3f, Point4f, Point3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- getPlaneThroughPoint(Point3f, Vector3f, Point4f) - Static method in class org.jmol.util.Measure
-
- getPlaneThroughPoints(Point3f, Point3f, Point3f, Vector3f, Vector3f, Vector3f, Point4f) - Static method in class org.jmol.util.Measure
-
- getPlot() - Method in class etomica.graphics.DisplayPlot
-
Accessor method to plot class so that its properties can be edited.
- getPlotSizeSlider(int) - Method in class etomica.graphics.DevicePlotPoints
-
Returns the plot scale slider for the given parameter (values can be
DevicePlotPoints.MIN_X, MAX_X, MIN_Y or MAX_Y.
- getPoint() - Method in class g3dsys.images.Ball
-
- getPoint() - Method in class g3dsys.images.Ellipse
-
- getPolarizationEnergy(IMoleculeList) - Method in class etomica.models.co2.PNCO2GCPM
-
This returns the polarizable portion of the GCPM potential for any
number of atoms.
- getPolarizationEnergy(IMoleculeList) - Method in class etomica.models.co2.PNGCPM
-
This returns the polarizable portion of the GCPM potential for any
number of atoms.
- getPolarizationEnergy(IMoleculeList) - Method in class etomica.models.water.PNWaterGCPM
-
This returns the polarizable portion of the GCPM potential for any
number of atoms.
- getPolarizationEnergy(IMoleculeList) - Method in interface etomica.potential.PotentialPolarizable
-
Returns the polarization contribution (non pairwise-additive) to the
energy for the given AtomSet.
- getPolytope() - Method in class etomica.graphics.DisplayPolytope
-
- getPoreCenters() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- getPoreDim() - Method in class etomica.space.BoundaryRectangularPore
-
Returns index of periodic dimension.
- getPoreRadius() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- getPos(int) - Method in class etomica.models.co2.P2CO2Hellmann
-
- getPosition() - Method in class etomica.atom.Atom
-
- getPosition() - Method in interface etomica.atom.IAtom
-
- getPosition() - Method in class etomica.lattice.LatticePlane
-
Returns the position i, such the the plane is located at the i-th from the origin.
- getPosition() - Method in class etomica.math.geometry.Hypersphere
-
- getPosition() - Method in class etomica.math.geometry.Polytope
-
Returns the geometric center of the polytope.
- getPosition() - Method in interface etomica.molecule.IMoleculePositioned
-
Returns the position of the IMolecule.
- getPosition() - Method in class etomica.molecule.MoleculeOriented
-
- getPositionDataInfo() - Method in interface etomica.data.DataSourcePositioned
-
- getPositionDataInfo() - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
-
- getPositionDefinition() - Method in class etomica.action.BoxImposePbc
-
- getPositionDefinition() - Method in class etomica.data.meter.MeterProfileByAtoms
-
- getPositionDefinition() - Method in class etomica.data.meter.MeterProfileByVolume
-
- getPositionDefinition() - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- getPositionDefinition() - Method in class etomica.normalmode.CoordinateDefinitionMolecule
-
- getPositionDefinition() - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- getPositionDefinition() - Method in class etomica.virial.CoordinatePairMoleculeSet
-
- getPositionSource() - Method in class etomica.data.meter.MeterProfile
-
Returns the RandomPositionSource used by this meter.
- getPositionSource() - Method in class etomica.data.meter.MeterWidomInsertion
-
Returns the RandomPositionSource used by this meter.
- getPositionSource() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
Returns the RandomPositionSource used by this move.
- getPositionSource() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
Returns the RandomPositionSource used by this move.
- getPositionSource() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
Returns the RandomPositionSource used by this meter.
- getPositionSource() - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Returns the RandomPositionSource used by this meter.
- getPositionSource() - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- getPositivePrefix() - Method in class etomica.util.ScientificFormat
-
- getPositiveSuffix() - Method in class etomica.util.ScientificFormat
-
- getPostAction() - Method in class etomica.action.SimulationRestart
-
- getPostAction() - Method in class etomica.graphics.Device
-
- getPotential() - Method in class etomica.chem.models.Model.PotentialAndIterator
-
- getPotential() - Method in class etomica.data.meter.MeterEnergy
-
- getPotential(ISpecies[]) - Method in class etomica.potential.PotentialMaster
-
Returns the potential that applies to the specified types,
or null of no existing potential applies.
- getPotential() - Method in class etomica.virial.ClusterSumIC.FR2
-
- getPotential() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getPotential() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getPotential() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getPotential() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getPotential() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getPotential() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getPotential() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getPotential() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getPotential() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getPotential() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getPotential() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getPotential() - Method in class etomica.virial.MayerD2FDT2Spherical
-
- getPotential() - Method in class etomica.virial.MayerDFDTSpherical
-
- getPotential() - Method in class etomica.virial.MayerDFQFHDTSpherical
-
- getPotential() - Method in class etomica.virial.MayerEGeneral
-
- getPotential() - Method in class etomica.virial.MayerENonGeneral
-
- getPotential() - Method in class etomica.virial.MayerESpherical
-
- getPotential() - Method in interface etomica.virial.MayerFunction
-
- getPotential() - Method in class etomica.virial.MayerFunctionProductGeneral
-
- getPotential() - Method in class etomica.virial.MayerFunctionSum
-
- getPotential() - Method in class etomica.virial.MayerFunctionSumGeneral
-
- getPotential() - Method in class etomica.virial.MayerFunctionTemperature
-
- getPotential() - Method in class etomica.virial.MayerGeneral
-
- getPotential() - Method in class etomica.virial.MayerGeneralAtomic
-
- getPotential() - Method in class etomica.virial.MayerGeneralSpherical
-
- getPotential() - Method in class etomica.virial.MayerHardSphere
-
- getPotential() - Method in class etomica.virial.MayerHSMixture
-
- getPotential() - Method in class etomica.virial.MayerPTAtt
-
- getPotential() - Method in class etomica.virial.MayerPUGeneral
-
- getPotential() - Method in class etomica.virial.MayerSphericalPTAtt
-
- getPotential() - Method in class etomica.virial.MayerSSSeries
-
- getPotential() - Method in class etomica.virial.MayerWell
-
- getPotential() - Method in class etomica.virial.MayerXSpherical
-
- getPotential() - Method in class etomica.virial.MuFGeneral
-
- getPotential() - Method in class etomica.virial.MuGeneral
-
- getPotential() - Method in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.MuDeltaEBond
-
- getPotential() - Method in class etomica.virial.simulations.VirialB3C1TIP4Pwater.MuFBond
-
- getPotential() - Method in class etomica.virial.simulations.VirialB3C2TIP4Pwater.fPlusBetaEU
-
- getPotential() - Method in class etomica.virial.simulations.VirialB3C2TIP4Pwater.MuProduct
-
- getPotential1BodyList(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- getPotential1BodyList(IAtom) - Method in class etomica.nbr.list.NeighborListManager
-
- getPotentialCalculation() - Method in class etomica.mappedvirial.MeterMappedU
-
- getPotentialCalculation() - Method in class etomica.mappedvirial.MeterMappedVirial
-
- getPotentialCalculation() - Method in class etomica.mappedvirial.MeterMappedVirialV
-
- getPotentialCalculations() - Method in interface etomica.threaded.IPotentialCalculationThreaded
-
- getPotentialCalculations() - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- getPotentialCollectionFactory() - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- getPotentialEnergy() - Method in class etomica.data.meter.MeterEnergy
-
- getPotentialEnergy() - Method in class etomica.integrator.IntegratorBox
-
- getPotentialEnergy() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- getPotentialGroupInterNonBondedLike() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- getPotentialGroupInterNonBondedUnlike() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- getPotentialGroupIntraBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- getPotentialIndex(IPotential) - Method in class etomica.potential.PotentialArray
-
Returns the index that this type has assigned to the given
potential.
- getPotentialIndex(IPotential) - Method in class etomica.potential.PotentialArrayByType
-
Returns the index that this type has assigned to the given
potential.
- getPotentialIndex(IPotentialMolecular) - Method in class etomica.potential.PotentialArrayMolecular
-
Returns the index that this type has assigned to the given
potential.
- getPotentialIntraBondedTorsion() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- getPotentialJList() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getPotentialJList() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getPotentialJListListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getPotentialJListListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getPotentialListDisplayLSM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getPotentialListDisplayLSM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getPotentialMaster() - Method in class etomica.integrator.IntegratorBox
-
- getPotentialMaster() - Method in class etomica.modules.vle.MeterPressure2
-
Returns the integrator associated with this instance.
- getPotentialMaster() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- getPotentialMasterCell() - Method in class etomica.nbr.PotentialMasterHybrid
-
- getPotentialMasterList() - Method in class etomica.nbr.PotentialMasterHybrid
-
- getPotentialMasters() - Method in class etomica.meta.wrappers.SimulationWrapper
-
- getPotentialMolecularNonBondedLike() - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularLike
-
- getPotentialMolecularUnlike() - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- getPotentialParamAndValuesString() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getPotentialParamDispayTable() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getPotentialParamDispayTable() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getPotentialParamDisplayLSM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getPotentialParamDisplayLSM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getPotentialParamDisplayTM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getPotentialParamDisplayTM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getPotentialParamDisplayTMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getPotentialParamDisplayTMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getPotentialParamString() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getPotentialPlus() - Method in class etomica.virial.MayerSphericalPlus
-
- getPotentialRange() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Returns the potential range.
- getPotentialRange() - Method in class etomica.nbr.cell.NeighborCellManager
-
Returns the potential range.
- getPotentials() - Method in class etomica.chem.models.Model
-
Returns an array of objects wrapping bonding Potentials and the
AtomsetIteratorBasisDependents that return atoms appropriate for those
potentials.
- getPotentials() - Method in class etomica.chem.models.ModelChain
-
- getPotentials() - Method in class etomica.potential.PotentialArray
-
- getPotentials() - Method in class etomica.potential.PotentialArrayByType
-
- getPotentials() - Method in class etomica.potential.PotentialArrayMolecular
-
- getPotentials() - Method in class etomica.potential.PotentialGroup
-
- getPotentials() - Method in class etomica.potential.PotentialMaster
-
Returns an array containing all molecular Potentials.
- getPotentials() - Method in class etomica.threaded.PotentialThreaded
-
- getPotentialsClassList() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getPotentialsCollectionBuilder() - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- getPotentialSiteAtIndex(int) - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getPotentialSiteAtIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getPotentialSites() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getPotentialSites(int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getPotentialSites() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getPotentialsList() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getPotentialsSelectedIndex() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getPreAction() - Method in class etomica.graphics.Device
-
Returns the action to be performed before the primary action executed
by the device.
- getPrecision() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
-
- getPrecision() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
-
- getPrecision() - Method in class etomica.graphics.DecimalSlider
-
Accessor method for precision of slider, defined as number of
digits after the decimal that will be distinguished by slider.
- getPrecision() - Method in class etomica.graphics.DeviceBox
-
Accessor method of the precision, which specifies the number of significant figures to be displayed.
- getPrecision() - Method in class etomica.graphics.DeviceSlider
-
- getPrecision() - Method in class etomica.graphics.DisplayTable
-
Accessor method of the precision, which specifies the number of
significant figures to be displayed.
- getPrecision() - Method in class etomica.graphics.DisplayTextBox
-
Accessor method of the precision, which specifies the number of significant figures to be displayed.
- getPrecision() - Method in class etomica.graphics.DisplayTextBoxesCAE
-
Accessor method of the precision, which specifies the number of significant figures to be displayed.
- getPrecision() - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
- getPrefix() - Method in class etomica.units.PrefixedUnit
-
- getPressure() - Method in class etomica.association.MCMoveVolumeAssociated
-
- getPressure() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- getPressure() - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- getPressure() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- getPressure() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- getPressure() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- getPressure() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- getPressure() - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- getPressure() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- getPressure() - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- getPressure() - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- getPressure() - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- getPressure(int, int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOS
-
- getPressure() - Method in class etomica.potential.P1HardMovingBoundary
-
- getPressure1() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- getPressure1XYZ() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- getPressureDimension() - Method in class etomica.association.MCMoveVolumeAssociated
-
- getPressureDimension() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- getPressureDimension() - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- getPressureDimension() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- getPressureDimension() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- getPressureDimension() - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- getPressureDimension() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- getPressureDimension() - Method in class etomica.potential.P1HardMovingBoundary
-
- getPressureSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- getPressureSumXYZ() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- getPressureTensor() - Method in class etomica.dimer.PotentialCalculationForcePressureSumGB
-
Returns the virial portion of pressure tensor calculated during the last
potential calculation.
- getPressureTensor() - Method in class etomica.integrator.IntegratorRigidIterative
-
Returns the pressure tensor based on the forces calculated during the
last time step.
- getPressureTensor() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
Returns the pressure tensor based on the forces calculated during the
last time step.
- getPressureTensor() - Method in class etomica.integrator.IntegratorVelocityVerlet
-
Returns the pressure tensor based on the forces calculated during the
last time step.
- getPressureTensor() - Method in class etomica.integrator.IntegratorVerlet
-
Returns the pressure tensor based on the forces calculated during the
last time step.
- getPressureTensor() - Method in class etomica.modules.droplet.IntegratorDroplet
-
Returns the pressure tensor based on the forces calculated during the
last time step.
- getPressureTensor() - Method in class etomica.potential.PotentialCalculationForcePressureSum
-
Returns the virial portion of pressure tensor calculated during the last
potential calculation.
- getPressureTensor() - Method in class etomica.potential.PotentialCalculationPressureTensor
-
Returns the pressure tensor based on a previous call to
PotentialMaster.calculate
- getPressureTensor() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
Returns the pressure tensor based on the forces calculated during the
last time step.
- getPrevX() - Method in class etomica.graphics.DisplayCanvas
-
- getPrevY() - Method in class etomica.graphics.DisplayCanvas
-
- getPrimitive() - Method in class etomica.lattice.BravaisLattice
-
Returns the primitive object used to construct this lattice.
- getPrimitive() - Method in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- getPrimitive() - Method in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- getPrimitive() - Method in class etomica.normalmode.CoordinateDefinition
-
- getPrimitiveFcc() - Method in class etomica.lattice.LatticeCubicFcc
-
Returns a new PrimitiveFcc instance corresponding to the fcc lattice.
- getPrimitiveHexagonal() - Method in class etomica.lattice.LatticeOrthorhombicHexagonal
-
Returns a new PrimitiveFcc instance corresponding to the fcc lattice.
- getPriority() - Method in class etomica.action.BoxImposePbc
-
- getPriority() - Method in class etomica.zeolite.MSDCoordWriter
-
- getPrivateKey() - Method in class org.jmol.g3d.Graphics3D
-
- getProductOfFrequencies() - Method in class etomica.action.CalcVibrationalModes
-
- getProfileDataInfo() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- getProfileDim() - Method in class etomica.data.meter.MeterProfile
-
Accessor method for vector describing the direction along which the profile is measured.
- getProfileDim() - Method in class etomica.data.meter.MeterProfileByAtoms
-
Accessor method for vector describing the direction along which the profile is measured.
- getProfileDim() - Method in class etomica.data.meter.MeterProfileByVolume
-
Accessor method for vector describing the direction along which the profile is measured.
- getProfileDim() - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- getPrompt() - Method in class etomica.graph.engine.ConsoleUI
-
- getProperty() - Method in class etomica.graph.engine.impl.CommandPropertyValueImpl
-
- getProperty() - Method in interface etomica.graph.engine.Parser.CommandPropertyValue
-
- getProperty() - Method in class etomica.graphics.DeviceSlider
-
- getProperty() - Method in class etomica.graphics.DeviceSpinner
-
- getProperty() - Method in class etomica.modifier.ModifierGeneral
-
- getProperty() - Method in class etomica.server.representations.PropertyUpdate
-
- getPropertyNames() - Method in interface etomica.graph.engine.Environment
-
- getPropertyNames() - Method in class etomica.graph.engine.impl.EnvironmentImpl
-
- getPropertyType() - Method in class etomica.meta.properties.ArrayProperty
-
- getPropertyType() - Method in class etomica.meta.properties.AtomListProperty
-
- getPropertyType() - Method in class etomica.meta.properties.InstanceProperty
-
- getPropertyType() - Method in class etomica.meta.properties.MoleculeListProperty
-
- getPropertyType() - Method in interface etomica.meta.properties.Property
-
- getPropertyType() - Method in class etomica.meta.properties.VectorProperty
-
- getPropertyValue(String) - Method in interface etomica.graph.engine.Environment
-
- getPropertyValue(String) - Method in class etomica.graph.engine.impl.EnvironmentImpl
-
- getPType() - Method in class etomica.models.nitrogen.SpeciesN2
-
- getPType() - Method in class etomica.models.nitrogen.SpeciesN2B
-
- getPType() - Method in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- getPump() - Method in class etomica.server.dao.DataStreamStore.DataPlumbing
-
- getPushInterval() - Method in class etomica.data.DataAccumulator
-
Accumulated data are pushed to the data sinks after every pushInterval calls
to putData.
- getPYCorrection(byte) - Static method in class etomica.virial.PYGenerator
-
Returns graphs included in the correction to the PY approximation at the
n-th order.
- getQ() - Method in class etomica.chem.electrostatics.Charge
-
- getQ() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- getQ() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- getQ(int) - Method in class etomica.models.co2.P2CO2Hellmann
-
- getQ() - Static method in class etomica.models.water.P2WaterSzalewicz
-
- getQ0() - Method in class etomica.math.Quaternion
-
Returns the q0 component of the Quaternion
- getQ1() - Method in class etomica.math.Quaternion
-
Returns the q1 component of the Quaternion
- getQ2() - Method in class etomica.math.Quaternion
-
Returns the q2 component of the Quaternion
- getQ3() - Method in class etomica.math.Quaternion
-
Returns the q3 component of the Quaternion
- getqp() - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- getQP_Q() - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- getQU() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- getQU() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- getQuadrupolarMomentSquare() - Method in class etomica.potential.P2LJQ
-
- getQuadrupolarMomentSquare() - Method in class etomica.potential.P2LJQQ
-
- getQuality() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getQuardricZ(double, double, double[], double[]) - Static method in class org.jmol.util.Quadric
-
- getQuaternion() - Method in class etomica.atom.AtomOrientedQuaternion
-
- getQuaternionFrame(Point3f, Tuple3f, Tuple3f) - Static method in class org.jmol.util.Quaternion
-
- getQuaternionFrameV(Vector3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Quaternion
-
- getQuotedAttribute(String, String) - Static method in class org.jmol.util.Parser
-
- getQuotedStringAt(String, int) - Static method in class org.jmol.util.Parser
-
- getQuotedStringNext(String, int[]) - Static method in class org.jmol.util.Parser
-
- getR0() - Method in class etomica.potential.P2Harmonic
-
Separation at which potential is at its minimum.
- getR0Dimension() - Method in class etomica.potential.P2Harmonic
-
- getr2(int, int) - Method in class etomica.virial.CoordinatePairLeafSet
-
Returns atom pair for ith and jth atoms in set.
- getr2(int, int) - Method in class etomica.virial.CoordinatePairMoleculeSet
-
Returns atom pair for ith and jth atoms in set.
- getr2(int, int) - Method in interface etomica.virial.CoordinatePairSet
-
Returns atom pair for ith and jth atoms in set.
- getr2d2udr2(int, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnPY_1QC_Helium
-
- getRadius() - Method in class etomica.math.geometry.Hypersphere
-
- getRadius() - Method in class etomica.potential.P1SoftBoundary
-
Returns the radius.
- getRadius(int) - Static method in class org.jmol.util.Quadric
-
- getRadiusDimension() - Method in class etomica.potential.P1SoftBoundary
-
- getRandom() - Method in class etomica.simulation.Simulation
-
- getRandomizeProbability() - Method in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- getRandomNumberGenerator() - Method in class etomica.association.AtomSourceRandomDimer
-
Returns the random number generator used to pick atoms
- getRandomNumberGenerator() - Method in class etomica.association.AtomSourceRandomSmer
-
Returns the random number generator used to pick atoms
- getRandomNumberGenerator() - Method in class etomica.association.MoleculeSourceRandomDimer
-
Returns the random number generator used to pick atoms
- getRandomNumberGenerator() - Method in class etomica.atom.AtomSourceRandomLeaf
-
Returns the random number generator used to pick atoms
- getRandomNumberGenerator() - Method in class etomica.atom.AtomSourceRandomSpecies
-
Returns the random number generator used to pick atoms
- getRandomNumberGenerator() - Method in class etomica.molecule.MoleculeSourceRandomMolecule
-
Returns the random number generator used to pick molecules
- getRandomSeeds() - Method in class etomica.simulation.Simulation
-
- getRandSeedArray() - Static method in class etomica.util.random.RandomNumberGeneratorUnix
-
Convenience method that returns an array of integers, useful as seeds to
another RNG.
- getRange() - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- getRange() - Method in class etomica.lattice.RectangularLatticeNbrIteratorSquare
-
Returns (a copy of) the array specifying the neighbor range.
- getRange() - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
Returns infinity.
- getRange() - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
Returns infinity.
- getRange() - Method in class etomica.meam.P2EAM
-
- getRange() - Method in class etomica.meam.PotentialCuLREP
-
- getRange() - Method in class etomica.meam.PotentialEAM
-
- getRange() - Method in class etomica.meam.PotentialEAM_LS
-
- getRange() - Method in class etomica.meam.PotentialEFS
-
- getRange() - Method in class etomica.meam.PotentialMEAM
-
- getRange() - Method in class etomica.models.co2.P2CO2H2OWheatley
-
- getRange() - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- getRange() - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- getRange() - Method in class etomica.models.co2.P2CO2Hellmann
-
- getRange() - Method in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- getRange() - Method in class etomica.models.co2.PNCO2GCPM
-
- getRange() - Method in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- getRange() - Method in class etomica.models.co2.PNGCPM
-
- getRange() - Method in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- getRange() - Method in class etomica.models.co2.PNGCPM.PNGCPMCached
-
- getRange() - Method in class etomica.models.nitrogen.P0LatticeEnergyCorrec
-
- getRange() - Method in class etomica.models.nitrogen.P2Nitrogen
-
- getRange() - Method in class etomica.models.nitrogen.P2NitrogenAB
-
- getRange() - Method in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- getRange() - Method in class etomica.models.nitrogen.P2NitrogenShellModel
-
- getRange() - Method in class etomica.models.nitrogen.PRotConstraint
-
- getRange() - Method in class etomica.models.water.P2Water3P
-
- getRange() - Method in class etomica.models.water.P2Water3PSoft
-
- getRange() - Method in class etomica.models.water.P2Water4P
-
- getRange() - Method in class etomica.models.water.P2Water4PSoft
-
- getRange() - Method in class etomica.models.water.P2WaterSzalewicz
-
- getRange() - Method in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- getRange() - Method in class etomica.models.water.P2WaterTIP4P
-
- getRange() - Method in class etomica.models.water.P2WaterTIP4PHardCore
-
- getRange() - Method in class etomica.models.water.PNWaterGCPM
-
- getRange() - Method in class etomica.models.water.PNWaterGCPM.PNWaterGCPMCached
-
- getRange() - Method in class etomica.modules.adsorption.P1Wall
-
- getRange() - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- getRange() - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- getRange() - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
- getRange() - Method in class etomica.modules.colloid.P1Wall
-
- getRange() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- getRange() - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
- getRange() - Method in class etomica.modules.droplet.P1Smash
-
- getRange() - Method in class etomica.modules.droplet.P2Cohesion
-
- getRange() - Method in class etomica.modules.materialfracture.P1Tension
-
- getRange() - Method in class etomica.modules.mu.P2SquareWellOneSide
-
- getRange() - Method in class etomica.modules.sam.P1Sinusoidal
-
- getRange() - Method in class etomica.modules.sam.P1WCAWall
-
- getRange() - Method in class etomica.nbr.cell.PotentialMasterCell
-
- getRange() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- getRange() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Returns the range that determines how far to look for neighbors.
- getRange() - Method in class etomica.nbr.list.NeighborListManager
-
- getRange() - Method in class etomica.nbr.list.PotentialMasterList
-
Returns the range that determines how far to look for neighbors.
- getRange() - Method in class etomica.nbr.PotentialMasterHybrid
-
- getRange() - Method in class etomica.normalmode.P1ConstraintNbr
-
- getRange() - Method in class etomica.normalmode.P1ConstraintNbrHcp
-
- getRange() - Method in class etomica.normalmode.P2XOrder
-
Returns infinity.
- getRange() - Method in class etomica.potential.EwaldSummation
-
- getRange() - Method in class etomica.potential.EwaldSummation.P2EwaldReal
-
- getRange() - Method in class etomica.potential.EwaldSumMolecules
-
- getRange() - Method in interface etomica.potential.IPotential
-
Returns the range over which the potential applies.
- getRange() - Method in class etomica.potential.P1ExternalField
-
- getRange() - Method in class etomica.potential.P1HardBoundary
-
- getRange() - Method in class etomica.potential.P1HydrogenMielke
-
- getRange() - Method in class etomica.potential.P22CLJQ
-
- getRange() - Method in class etomica.potential.P2CO2EMP
-
- getRange() - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- getRange() - Method in class etomica.potential.P2DLPOLY
-
- getRange() - Method in class etomica.potential.P2DoubleWell
-
- getRange() - Method in class etomica.potential.P2EffectiveFeynmanHibbs
-
- getRange() - Method in class etomica.potential.P2HardAssociation
-
Returns the well diameter.
- getRange() - Method in class etomica.potential.P2HardAssociationCone
-
Returns infinity.
- getRange() - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Returns infinity.
- getRange() - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Returns infinity.
- getRange() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Returns infinity.
- getRange() - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Returns infinity.
- getRange() - Method in class etomica.potential.P2HardAssociationConeReference
-
Returns infinity.
- getRange() - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
-
Returns infinity.
- getRange() - Method in class etomica.potential.P2HardAssociationConeSW
-
Returns sigma * cutoffFactor.
- getRange() - Method in class etomica.potential.P2HardBond
-
Returns infinity.
- getRange() - Method in class etomica.potential.P2HardBondedList
-
- getRange() - Method in class etomica.potential.P2HardSphere
-
- getRange() - Method in class etomica.potential.P2HardWrapper
-
- getRange() - Method in class etomica.potential.P2HePCKLJS.P2HeQFH
-
- getRange() - Method in class etomica.potential.P2HePCKLJS.P2HeTI
-
- getRange() - Method in class etomica.potential.P2HeSimplified.P2HeQFH
-
- getRange() - Method in class etomica.potential.P2HeSimplified.P2HeTI
-
- getRange() - Method in class etomica.potential.P2HSDipole
-
- getRange() - Method in class etomica.potential.P2HydrogenHinde
-
- getRange() - Method in class etomica.potential.P2HydrogenHindeAtomic
-
- getRange() - Method in class etomica.potential.P2HydrogenHindePatkowski
-
- getRange() - Method in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- getRange() - Method in class etomica.potential.P2HydrogenPatkowski
-
- getRange() - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- getRange() - Method in class etomica.potential.P2Ideal
-
Returns zero.
- getRange() - Method in class etomica.potential.P2LJDipole
-
- getRange() - Method in class etomica.potential.P2LJQ
-
- getRange() - Method in class etomica.potential.P2MoleculeMonatomic
-
- getRange() - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
Returns the truncation radius.
- getRange() - Method in class etomica.potential.P2MoleculeTruncated
-
Returns the truncation radius.
- getRange() - Method in class etomica.potential.P2NitrogenHellmann
-
- getRange() - Method in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- getRange() - Method in class etomica.potential.P2O2Bartolomei
-
- getRange() - Method in class etomica.potential.P2O2Bartolomei.P2O2TI
-
- getRange() - Method in class etomica.potential.P2PenetrableBond
-
Returns infinity.
- getRange() - Method in class etomica.potential.P2PenetrableSphere
-
- getRange() - Method in class etomica.potential.P2PenetrableSquareWell
-
- getRange() - Method in class etomica.potential.P2QChem
-
- getRange() - Method in class etomica.potential.P2ReactionFieldDipole
-
The radius of the sphere within which molecules contribute to the reaction
field of a given molecule.
- getRange() - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- getRange() - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- getRange() - Method in class etomica.potential.P2SemiclassicalAtomic
-
- getRange() - Method in class etomica.potential.P2SemiclassicalMolecular
-
- getRange() - Method in class etomica.potential.P2SoftSphericalTruncated
-
Returns the truncation radius.
- getRange() - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
Returns the truncation radius.
- getRange() - Method in class etomica.potential.P2SoftTruncated
-
Returns the truncation radius.
- getRange() - Method in class etomica.potential.P2SpheroPolyhedron
-
- getRange() - Method in class etomica.potential.P2SquareWell
-
- getRange() - Method in class etomica.potential.P2SquareWellRobust
-
- getRange() - Method in class etomica.potential.P2Tether
-
Returns the tether length.
- getRange() - Method in class etomica.potential.P2TriangleWell
-
- getRange() - Method in class etomica.potential.P2WaterPotentialsJankowski
-
- getRange() - Method in class etomica.potential.P2WCA
-
Returns the range of the potential, which is the point of truncation.
- getRange() - Method in class etomica.potential.P3AxilrodTeller
-
- getRange() - Method in class etomica.potential.P3BondAngle
-
- getRange() - Method in class etomica.potential.P3BondAngleDreiding
-
- getRange() - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- getRange() - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- getRange() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- getRange() - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- getRange() - Method in class etomica.potential.P3HydrogenATM
-
- getRange() - Method in class etomica.potential.P3HydrogenManzhos
-
- getRange() - Method in class etomica.potential.P3Induction
-
- getRange() - Method in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- getRange() - Method in class etomica.potential.P4BondTorsion
-
- getRange() - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- getRange() - Method in class etomica.potential.P4TorsionDreiding
-
- getRange() - Method in class etomica.potential.Potential
-
- getRange() - Method in class etomica.potential.Potential0
-
Returns zero.
- getRange() - Method in class etomica.potential.Potential1
-
Returns zero.
- getRange() - Method in class etomica.potential.Potential2SoftSpherical
-
Returns infinity.
- getRange() - Method in class etomica.potential.Potential2SoftSphericalLS
-
Returns infinity.
- getRange() - Method in class etomica.potential.PotentialAtomicSum
-
- getRange() - Method in class etomica.potential.PotentialDLPOLY
-
- getRange() - Method in class etomica.potential.PotentialEmul
-
- getRange() - Method in class etomica.potential.PotentialGroup
-
Returns the maximum of the range of all potentials in the group.
- getRange() - Method in class etomica.potential.PotentialMolecular
-
- getRange() - Method in class etomica.potential.PotentialMolecularMonatomic
-
- getRange() - Method in class etomica.potential.PotentialMolecularSum
-
- getRange() - Method in class etomica.potential.PotentialNonAdditiveDifference
-
- getRange() - Method in class etomica.rotation.P2LJDipole
-
- getRange() - Method in class etomica.spin.P2Spin
-
Returns 0, becuase potential operates on a lattice and range
should not be needed.
- getRange() - Method in class etomica.threaded.PotentialThreaded
-
- getRange() - Method in class etomica.virial.P1IntraLambda
-
- getRange() - Method in class etomica.virial.PotentialCommonAtomic
-
- getRange() - Method in class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
-
- getRange() - Method in class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
-
- getRange() - Method in class etomica.virial.PotentialNonAdditive
-
- getRange() - Method in class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
-
- getRange() - Method in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
-
- getRange() - Method in class etomica.yukawa.P2HC2Yukawa
-
- getRangedPotentials(ISpecies) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- getRangedPotentials(AtomType) - Method in class etomica.nbr.PotentialMasterNbr
-
- getRatios() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
-
Returns overlap sampling results (ratio of partition functions between
sequential number of atoms).
- getRawData() - Method in class etomica.data.AccumulatorAverageBlockless
-
- getRawData() - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
- getRawData() - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getRawData() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getRawDataBlockSize() - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getRawDataBlockSize() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getRawLogAccumulator() - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getRawLogAccumulator() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getRawLogDataCorrelation() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Returns the correlation between consecutive values of the log of the "raw"
data held by the accumulator.
- getRCut() - Method in class etomica.potential.EwaldSummation
-
Returns real-space cutoff
- getRdf() - Method in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- getrdfdr(int, double, double) - Static method in class etomica.virial.BnHNCLJ
-
- getrdfdr(int, double, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnIETP2Spherical
-
- getrdfdr(int, double, double) - Static method in class etomica.virial.BnPYLJ
-
- getrdfdr(int, double, double) - Static method in class etomica.virial.BnSCALJ
-
- getrdudr(int, double, Potential2SoftSpherical) - Static method in class etomica.virial.BnPY_1QC_Helium
-
- getRe() - Method in class etomica.potential.P2ModifiedMorse
-
- getRe() - Method in class etomica.potential.P2Morse
-
- getReal() - Method in class etomica.math.numerical.FastFourierTransform
-
array value calls
- getRealEigenvalues() - Method in class etomica.eigenstuff.MyEigenvalueDecomposition
-
Return the real parts of the eigenvalues
- getRealEigenvalues() - Method in class org.jmol.util.Eigen
-
Return the real parts of the eigenvalues
- getReferenceDataInterval() - Method in class etomica.normalmode.SimOverlapModule
-
- getRefPref() - Method in class etomica.normalmode.MeterSamplingHarmonic
-
- getRefPref() - Method in class etomica.normalmode.MeterSamplingTarget
-
- getRefPref() - Method in class etomica.normalmode.MeterWorkBennetHarmonic
-
- getRefPref() - Method in class etomica.normalmode.MeterWorkBennetTarget
-
- getRefPref() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- getRefPref() - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- getRefPref() - Method in class etomica.normalmode.MeterWorkTargetBennet
-
- getRefPref() - Method in class etomica.normalmode.MeterWorkTargetUmbrella
-
- getRefPref() - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- getRefPref() - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- getRefPref() - Method in class etomica.normalmode.SimBennet
-
- getRefPref() - Method in class etomica.normalmode.SimHarmonicUmbrella
-
- getRefPref() - Method in class etomica.normalmode.SimTargetUmbrella
-
- getRefPref() - Method in class etomica.normalmode.SimUmbrella
-
- getRefPref() - Method in class etomica.normalmode.SimUmbrellaSoftSphere
-
- getRefSource() - Method in class etomica.overlap.DataOverlap
-
Returns object capable of retrieving data from the reference system.
- getRefStepFraction() - Method in class etomica.overlap.IntegratorOverlap
-
- getRefTimeFraction() - Method in class etomica.overlap.IntegratorOverlap
-
- getReinitButton() - Method in class etomica.graphics.DeviceTrioControllerButton
-
- getRelativeDisplacement(IAtom) - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- getRelaxationRateH() - Method in class etomica.integrator.IntegratorGear4NPH
-
- getRelaxationRateHDimension() - Method in class etomica.integrator.IntegratorGear4NPH
-
- getRelaxationRateP() - Method in class etomica.integrator.IntegratorGear4NPH
-
- getRelaxationRatePDimension() - Method in class etomica.integrator.IntegratorGear4NPH
-
- getRemove() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getRemoveSpecies1() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getRemoveSpecies2() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getRemoveSpecies3() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getRenderHeight() - Method in class org.jmol.util.GData
-
gets g3d height
- getRenderWidth() - Method in class org.jmol.util.GData
-
gets g3d width
- getReset() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getReset() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getResetAction() - Method in class etomica.graphics.DeviceNSelector
-
Returns the action used to "reset" the simulation after changing the
number of molecules, SimulationRestart by default.
- getResetAveragesButton() - Method in class etomica.graphics.DeviceTrioControllerButton
-
- getResizeOnNewBox() - Method in class etomica.graphics.DisplayBox
-
Get the flag indicating whether the graphic should resize from its
currently displayed size when a new box is set.
- getResults(Potential2SoftSpherical, double, double, double, boolean) - Static method in class etomica.virial.B2ForSphericallySymmetricUByTrapezoidRule
-
- getReverseEdgeColor(char) - Static method in class etomica.graph.model.impl.MetadataImpl
-
- getRm() - Method in class etomica.potential.P2Exp6Buckingham
-
- getRmax() - Method in class etomica.potential.P2Exp6Buckingham
-
- getRmsd(Point3f[][], Quaternion) - Static method in class org.jmol.util.Measure
-
- getRmSquared() - Method in class etomica.potential.P2Exp6Buckingham
-
- getRootColorMap() - Method in class etomica.graph.engine.impl.ConstructorColoredImpl
-
- getRootColorMap() - Method in interface etomica.graph.engine.Parser.ConstructorColored
-
- getRootNodes() - Method in class etomica.graph.engine.impl.ConstructorMonoImpl
-
- getRootNodes() - Method in interface etomica.graph.engine.Parser.ConstructorMono
-
- getRotationAxis() - Method in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
-
- getRotationMatrix() - Method in class etomica.math.Quaternion
-
Returns the rotation matrix associated with the Quaternion q as a Jama.Matrix
- getRotationScale(Matrix3f) - Method in class org.jmol.util.Matrix4f
-
Gets the upper 3x3 values of this matrix and places them into the matrix
m1.
- getRow(int, float[]) - Method in class org.jmol.util.Matrix3f
-
Copies the matrix values in the specified row into the array parameter.
- getRow(int, float[]) - Method in class org.jmol.util.Matrix4f
-
Copies the matrix values in the specified row into the array parameter.
- getRowCount() - Method in class etomica.data.DataSinkTable
-
Returns the length of the longest column.
- getRowCount() - Method in class etomica.graphics.DeviceTableModelGeneric
-
Get the number of rows in the table (including blank rows).
- getRowCount() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- getRowCount() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- getRowCount() - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- getRowHeader(int) - Method in class etomica.data.DataSinkTable
-
- getRowHeader(int) - Method in class etomica.data.types.DataTable.DataInfoTable
-
Returns the row header for row i or an empty string if there are no
row headers.
- getRowHeaders() - Method in class etomica.data.types.DataTable.DataInfoTableFactory
-
Returns a copy of the row headers or null if no row headers exist.
- getRowLabelColumnHeader() - Method in class etomica.graphics.DisplayTable
-
Returns the header of the row-label column.
- getRowLabels() - Method in class etomica.graphics.DisplayTable
-
Descriptive text for each row.
- getRPow() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
-
- getRun() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getRun() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getSafetyFactor() - Method in class etomica.nbr.CriterionPositionWall
-
returns the safety factor
- getSafetyFactor() - Method in class etomica.nbr.CriterionSimple
-
- getSafetyFactor() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Returns the safety factor.
- getSafetyFactor() - Method in class etomica.nbr.list.PotentialMasterList
-
Returns the safety factor.
- getSafetyFactor() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- getSampleCluster() - Method in class etomica.virial.BoxCluster
-
returns the cluster used for sampling in this box
- getSampleClusters() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- getSampleCount() - Method in class etomica.data.AccumulatorAverage
-
- getSampleCount() - Method in class etomica.data.AccumulatorAverageBlockless
-
- getSampleCount() - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
- getSampleCount() - Method in interface etomica.data.history.History
-
Returns the number of data samples currently held by the History.
- getSampleCount() - Method in class etomica.data.history.HistoryCollapsing
-
- getSampleCount() - Method in class etomica.data.history.HistoryComplete
-
- getSampleCount() - Method in class etomica.data.history.HistoryScrolling
-
- getSampleCount() - Method in interface etomica.overlap.DataOverlap.DataSourceOverlapAvg
-
- getSampleCount() - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsing
-
- getSampleCount() - Method in class etomica.overlap.DataOverlap.DataSourceOverlapAvgSimple
-
- getSampleLogVariance() - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getSampleLogVariance() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getSampleVariance() - Method in class etomica.data.AccumulatorAverageBootstrap
-
- getSampleVariance() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- getSaveValues() - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- getSaveValues() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- getSBOType() - Method in class etomica.models.OPLS.SpeciesAceticAcid
-
- getScalar() - Method in class etomica.math.Quaternion
-
Returns the scalar part of the Quaternion
- getScalarEnergy() - Method in class etomica.conjugategradient.DerivativeEnergyFunction
-
- getScale() - Method in class etomica.action.BoxInflate
-
- getScale() - Method in class etomica.graphics.DisplayBox
-
- getScale() - Method in class etomica.graphics.DisplayPolytope
-
- getScaledCoordinates() - Method in class etomica.lattice.crystal.Basis
-
Returns scaled coordinates
- getScaling() - Method in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- getScaling() - Method in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- getScalingDataSource() - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
Returns the data source for volume scalings.
- getScreenImage() - Method in class org.jmol.g3d.Graphics3D
-
- getScreenImage() - Method in class org.jmol.util.GData
-
- getSecondaryDirection() - Method in interface etomica.space3d.IOrientationFull3D
-
Returns a unit vector pointing in the orientation's secondary direction.
- getSecondaryDirection() - Method in class etomica.space3d.OrientationFull3D
-
- getSecondVector() - Method in class etomica.config.ConformationChainZigZag
-
- getSecondVector() - Method in class etomica.config.ConformationChainZigZag2
-
- getSecurityOff() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Returns whether or not scripts will be run securely
- getSeed() - Method in class etomica.util.random.RandomMersenneTwister
-
- getSeedArray() - Method in class etomica.util.random.RandomMersenneTwister
-
- getSeen() - Method in class etomica.graph.traversal.AbstractTraversal
-
- getSegments() - Method in class etomica.graph.property.FFTDecomposition
-
- getSelectedMove() - Method in class etomica.integrator.mcmove.MCMoveManager
-
- getSelectedRows() - Method in class etomica.graphics.DeviceTable
-
Returns the indices of all the selected rows on the table.
- getSelectedSpecies() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSelector() - Method in class etomica.graphics.DeviceSelector
-
- getSelector() - Method in class etomica.graphics.DeviceThermoSelector
-
- getSet(GraphIterator) - Method in class etomica.graph.iterators.IteratorToSet
-
- getSettableTokFromString(String) - Static method in class org.jmol.script.Token
-
- getSgima() - Method in class etomica.potential.P1HardPeriodic
-
- getShadeIndex(short) - Method in class org.jmol.g3d.Graphics3D
-
- getShadeIndex(float, float, float) - Static method in class org.jmol.util.Shader
-
- getShadeIndexNormalized(float, float, float) - Static method in class org.jmol.util.Shader
-
- getShades(short) - Static method in class org.jmol.util.Colix
-
- getShades(short) - Method in class org.jmol.util.GData
-
- getShades(int, boolean) - Static method in class org.jmol.util.Shader
-
- getShadesArgb(int, boolean) - Static method in class org.jmol.util.Colix
-
- getShadesGreyscale(short) - Static method in class org.jmol.util.Colix
-
- getShakeAgentManager() - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- getShakeTolerance() - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- getShape() - Method in class etomica.data.meter.MeterLocalDensity
-
- getShape() - Method in class etomica.data.meter.MeterLocalMoleFraction
-
Returns the subvolume shape for the mole fraction calculation.
- getShape() - Method in class etomica.graphics.DeviceTrioControllerButton
-
- getShape() - Method in class etomica.space.Boundary
-
- getShapeClassName(int, boolean) - Static method in class org.jmol.viewer.JmolConstants
-
- getShapeOrigin() - Method in class etomica.data.meter.MeterLocalMoleFraction
-
Returns the origin of the subvolume.
- getShapeVisibilityFlag(int) - Static method in class org.jmol.viewer.JmolConstants
-
- getShearRate() - Method in class etomica.modules.rheology.IntegratorPolymer
-
- getShearRateNumber() - Method in class etomica.modules.rheology.IntegratorPolymer
-
- getShift() - Method in class etomica.interfacial.ConfigurationLammps
-
- getShifts(Boundary, Vector, double) - Method in class etomica.graphics.OverflowShift
-
Provides information needed so that drawing can be done of portions of
the periodic images of an atom that overflow into the volume (because the
periodic image is just outside the volume).
- getShiftX() - Method in class etomica.graphics.DisplayCanvas
-
- getShiftY() - Method in class etomica.graphics.DisplayCanvas
-
- getShowBoundary() - Method in class etomica.graphics.DisplayBox
-
Get the flag indicating if the boundary should be drawn.
- getShowSlider() - Method in class etomica.graphics.DeviceSlider
-
- getShowValues() - Method in class etomica.graphics.DeviceSlider
-
- getSigma() - Method in class etomica.models.water.P2Water3P
-
- getSigma() - Method in class etomica.models.water.P2Water3PSoft
-
- getSigma() - Method in class etomica.models.water.P2Water4P
-
- getSigma() - Method in class etomica.models.water.P2Water4PSoft
-
- getSigma() - Method in class etomica.models.water.P2WaterTIP4P
-
- getSigma() - Method in class etomica.models.water.P2WaterTIP4PHardCore
-
- getSigma() - Method in class etomica.modules.adsorption.P1Wall
-
- getSigma() - Method in class etomica.modules.colloid.P1Wall
-
- getSigma() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
Returns the radius.
- getSigma() - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
Returns the radius.
- getSigma() - Method in class etomica.modules.sam.P1WCAWall
-
Returns the radius.
- getSigma() - Method in class etomica.modules.vle.VLESim
-
- getSigma() - Method in class etomica.potential.P22CLJQ
-
- getSigma() - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for Lennard-Jones size parameter
- getSigma() - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for Lennard-Jones size parameter
- getSigma() - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for Lennard-Jones size parameter
- getSigma() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for Lennard-Jones size parameter
- getSigma() - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for Lennard-Jones size parameter
- getSigma() - Method in class etomica.potential.P2HardAssociationConeReference
-
Accessor method for Lennard-Jones size parameter
- getSigma() - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
-
Accessor method for Lennard-Jones size parameter
- getSigma() - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for Lennard-Jones size parameter
- getSigma() - Method in class etomica.potential.P2HSDipole
-
- getSigma() - Method in class etomica.potential.P2LennardJones
-
Accessor method for Lennard-Jones size parameter.
- getSigma() - Method in class etomica.potential.P2LennardJonesDreiding
-
Accessor method for Lennard-Jones size parameter.
- getSigma() - Method in class etomica.potential.P2LJDipole
-
- getSigma() - Method in class etomica.potential.P2LJQ
-
- getSigma() - Method in class etomica.potential.P2LJQQ
-
- getSigma() - Method in class etomica.potential.P2SoftSphere
-
Accessor method for soft-sphere size parameter.
- getSigma() - Method in class etomica.potential.P2WCA
-
Accessor method for the size parameter.
- getSigma() - Method in class etomica.rotation.P2LJDipole
-
- getSigma() - Method in class etomica.units.systems.LJ
-
- getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getSigma(int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getSigma() - Method in class etomica.virial.MayerEHardSphere
-
Returns the HS diameter.
- getSigma() - Method in class etomica.virial.MayerHardSphere
-
Returns the HS diameter.
- getSigma(int, int) - Method in class etomica.virial.MCMoveClusterAtomHSChain
-
- getSigma(int, int) - Method in class etomica.virial.MCMoveClusterAtomHSChainMix
-
- getSigma(int, int) - Method in class etomica.virial.MCMoveClusterAtomHSTree
-
- getSigma(int, int) - Method in class etomica.virial.MCMoveClusterAtomHSTreeMix
-
- getSigma(int, int) - Method in class etomica.virial.MCMoveClusterAtomSQWChain
-
- getSigma(int, int) - Method in class etomica.virial.MCMoveClusterAtomSQWTree
-
- getSigma() - Method in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
-
- getSigma() - Method in class etomica.yukawa.P2HC2Yukawa
-
Accessor methods for size and energy parameters.
- getSigmaC() - Method in class etomica.potential.P2CO2EMP
-
- getSigmaCO() - Method in class etomica.potential.P2CO2EMP
-
- getSigmaColloid() - Method in class etomica.modules.colloid.ConfigurationColloid
-
- getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationCone
-
- getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSites
-
- getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
- getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeOneSite
-
- getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeReference
-
- getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeReferenceFourSites
-
- getSigmaDimension() - Static method in class etomica.potential.P2HardAssociationConeSW
-
- getSigmaDimension() - Method in class etomica.potential.P2LennardJones
-
- getSigmaDimension() - Method in class etomica.potential.P2LennardJonesDreiding
-
- getSigmaDimension() - Method in class etomica.potential.P2ModifiedMorse
-
- getSigmaDimension() - Method in class etomica.potential.P2Morse
-
- getSigmaDimension() - Method in class etomica.potential.P2SoftSphere
-
- getSigmaDimension() - Method in class etomica.potential.P2WCA
-
- getSigmaHSRef(int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getSigmaHSRef() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getSigmaHSRefField(int) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- getSigmaHSRefFieldA() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- getSigmaHSRefFieldB() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- getSigmaHSRefFieldC() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- getSigmaHSRefSpecies(IMolecularModel_SpeciesFactory) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- getSigmaMonomer() - Method in class etomica.modules.colloid.ConfigurationColloid
-
- getSigmaO() - Method in class etomica.potential.P2CO2EMP
-
- getSignature(Graph) - Method in class etomica.graph.iterators.filters.GlobalFilter.SignatureMaker
-
- getSignature() - Method in interface etomica.graph.model.Graph
-
- getSignature() - Method in class etomica.graph.model.impl.GraphImpl
-
- getSimEnvController() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- getSimId() - Method in class etomica.server.dao.DataStreamStore.DataPlumbing
-
- getSimRestart() - Method in class etomica.graphics.DeviceTrioControllerButton
-
- getSimulation() - Method in interface etomica.action.SimulationAction
-
- getSimulation() - Method in class etomica.action.SimulationActionAdapter
-
- getSimulation() - Method in class etomica.graphics.DeviceTrioControllerButton
-
Returns the simulation affected by the buttons.
- getSimulation() - Method in class etomica.graphics.SimulationGraphic
-
- getSimulation() - Method in class etomica.meta.SimulationModel
-
- getSimulation() - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
Returns the simulation associated with this PotentialMaster
- getSimulation() - Method in interface etomica.simulation.SimulationContainer
-
- getSimulation() - Method in class etomica.simulation.SimulationEvent
-
- getSite(IAtom) - Method in class etomica.nbr.site.NeighborSiteManager
-
- getSite() - Method in enum etomica.virial.GUI.models.EnumSiteName
-
- getSiteDisplacementIndex() - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- getSiteDisplacementIndex(Vector) - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- getSiteFactor() - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- getSiteManager() - Method in class etomica.normalmode.CoordinateDefinition
-
- getSites(Space) - Static method in class etomica.models.water.P2WaterSzalewicz
-
- getSitesNotParticipating(IMolecularModel_SpeciesFactory) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- getSitesOnSpecies() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSize() - Method in class etomica.graphics.DisplayBox
-
Gets the size of the box graphic.
- getSize() - Method in class etomica.lattice.crystal.Primitive
-
Returns a new array with values equal to the lengths of the primitive vectors.
- getSize() - Method in interface etomica.lattice.FiniteLattice
-
Returns an array with elements giving the maximum number of
index values in each dimension.
- getSize() - Method in class etomica.lattice.RectangularLattice
-
- getSizeA() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- getSizeA() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- getSizeA() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
- getSizeA() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- getSizeAB() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- getSizeAB() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- getSizeAB() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- getSizeABC() - Method in class etomica.lattice.crystal.PrimitiveCubic
-
Returns the common length of all primitive vectors.
- getSizeB() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- getSizeB() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- getSizeB() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- getSizeC() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- getSizeC() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- getSizeC() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- getSizeC() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- getSizeC() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- getSizeIncreaseRatio() - Static method in class etomica.atom.AtomArrayList
-
- getSizeIncreaseRatio() - Static method in class etomica.molecule.MoleculeArrayList
-
- getSkewLog() - Method in class etomica.data.AccumulatorAverageBootstrap
-
Returns the standard deviation of the log of the block averages, for all
block sizes.
- getSkewLog() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Returns the standard deviation of the log of the block averages, for all
block sizes.
- getSlab() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Get depth percentage
- getSlab() - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Get depth percentage
- getSlab() - Method in class org.jmol.util.GData
-
gets g3d slab
- getSlabColor() - Method in class org.jmol.util.MeshSurface
-
- getSlabObject(int, Object, boolean, Object) - Static method in class org.jmol.util.MeshSurface
-
- getSlabPercent() - Method in class g3dsys.control.G3DSys
-
- getSlabTranslucency() - Method in class org.jmol.util.MeshSurface
-
- getSlabType() - Method in class org.jmol.util.MeshSurface
-
- getSlabWithinRange(float, float) - Static method in class org.jmol.util.MeshSurface
-
- getSleepPeriod() - Method in class etomica.action.activity.ActivityIntegrate
-
Amount of time that thread is kept in sleep state after
each doStep done on integrator.
- getSlider(String) - Method in class etomica.graphics.DevicePlotPoints
-
Returns the slider for the given parameter.
- getSlider() - Method in class etomica.graphics.DeviceSlider
-
- getSlitDim() - Method in class etomica.space.BoundaryRectangularSlit
-
Returns index of non-periodic dimension.
- getSnapshotTime() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Returns the document to to seek to before rasterizing.
- getSoftBDcount() - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
- getSoftBDfrac() - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
- getSoftcount() - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
- getSoluteMoleFraction() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- getSoluteMoleFraction() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
Returns the mole fraction of solutes within the solute chamber.
- getSolutionChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- getSolutionChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
Returns the number density of the solution chamber
- getSolventChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- getSolventChamberDensity() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
Returns the number density of the solvent chamber
- getSolventThermoFrac() - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
Returns the fraction of well energy that is gained or lost by an atom
pair when they hop in or leave their well.
- getSources() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getSpace() - Method in class etomica.box.Box
-
- getSpace() - Method in class etomica.config.ConfigurationLattice.MyLattice
-
- getSpace() - Method in class etomica.data.types.DataTensor.DataInfoTensor
-
- getSpace() - Method in class etomica.data.types.DataTensor.DataInfoTensorFactory
-
Returns the Space
- getSpace() - Method in class etomica.data.types.DataVector.DataInfoVector
-
- getSpace() - Method in class etomica.data.types.DataVector.DataInfoVectorFactory
-
Returns the Space
- getSpace() - Method in class etomica.lattice.BravaisLattice
-
- getSpace() - Method in class etomica.lattice.crystal.Primitive
-
- getSpace() - Method in interface etomica.lattice.SpaceLattice
-
- getSpace() - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
-
- getSpace() - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
-
- getSpace() - Method in class etomica.simulation.Simulation
-
- getSpace() - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- getSpace() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getSpace() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getSpace() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getSpace() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- getSpace() - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- getSpace() - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- getSpace() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getSpace() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- getSpace() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getSpace() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- getSpacePosition() - Method in class etomica.lattice.LatticePlane
-
Gets the position of the plane as the distance from the
origin in the direction of the normal.
- getSpecialAtomName(int) - Static method in class org.jmol.viewer.JmolConstants
-
- getSpecies() - Method in class etomica.atom.AtomType
-
- getSpecies() - Method in class etomica.box.BoxMoleculeCountEvent
-
- getSpecies() - Method in class etomica.chem.models.Model
-
Returns the species associated with this Model, if it has already been
created.
- getSpecies() - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
-
Returns the ISpecies for which the chemical potential is to be measured.
- getSpecies() - Method in class etomica.data.meter.MeterDensity
-
- getSpecies() - Method in class etomica.data.meter.MeterLocalMoleFraction
-
Accessor method to get the current value of the species index
- getSpecies() - Method in class etomica.data.meter.MeterMoleFraction
-
- getSpecies() - Method in class etomica.data.meter.MeterNMolecules
-
- getSpecies() - Method in class etomica.data.meter.MeterProfileByAtoms
-
- getSpecies() - Method in class etomica.data.meter.MeterProfileByVolume
-
- getSpecies() - Method in class etomica.data.meter.MeterWidomInsertion
-
Accessor for the species for which chemical potential is evaluated
- getSpecies() - Method in class etomica.graphics.DeviceNSelector
-
- getSpecies() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- getSpecies() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
Accessor method for the set of species that can participate in an exchange move.
- getSpecies() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
Accessor for the species for which chemical potential is evaluated
- getSpecies() - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Accessor for the species for which chemical potential is evaluated
- getSpecies() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- getSpecies() - Method in class etomica.models.nitrogen.P0LatticeEnergyCorrec
-
- getSpecies() - Method in class etomica.modules.rosmosis.MeterFlux
-
- getSpecies() - Method in class etomica.nbr.molecule.CriterionSpecies
-
Returns the Species accepted by this criterion.
- getSpecies() - Method in class etomica.nbr.molecule.CriterionSpeciesPair
-
Returns the Species accepted by this NeighborCriterionMolecular
- getSpecies() - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
- getSpecies() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- getSpecies() - Method in class etomica.parser.ParmedStructure
-
- getSpecies(IPotentialMolecular) - Method in class etomica.potential.PotentialMaster
-
- getSpecies(int) - Method in class etomica.simulation.Simulation
-
Returns one of the simulation ISpecies.
- getSpecies() - Method in class etomica.simulation.SimulationSpeciesEvent
-
- getSpecies(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- getSpecies1() - Method in class etomica.config.ConfigurationZincblende
-
- getSpecies2() - Method in class etomica.config.ConfigurationZincblende
-
- getSpeciesAFixed() - Method in class etomica.config.GrainBoundaryConfiguration
-
- getSpeciesAllocation(ISpecies) - Method in class etomica.config.ConfigurationLatticeWithPlane
-
Sets the initial allocation of the species on the left side
of the plane.
- getSpeciesAMobile() - Method in class etomica.config.GrainBoundaryConfiguration
-
- getSpeciesBFixed() - Method in class etomica.config.GrainBoundaryConfiguration
-
- getSpeciesBMobile() - Method in class etomica.config.GrainBoundaryConfiguration
-
- getSpeciesco2Potentialslist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSpeciesCount() - Method in class etomica.simulation.Simulation
-
- getSpeciesCount1() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getSpeciesCount2() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getSpeciesCount3() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getSpeciesDataModel(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- getSpeciesDataModel() - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- getSpeciesDM() - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- getSpeciesethanePotentiallist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSpeciesh2oPotentiallist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSpeciesID() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- getSpeciesID() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- getSpeciesID() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- getSpeciesIdentifier(int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSpeciesIndex() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- getSpeciesIndex() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- getSpeciesIndex(int) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- getSpeciesIndex() - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularLike
-
- getSpeciesIndex() - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- getSpeciesIndex(int) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- getSpeciesInteractionIndex() - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- getSpeciesJList() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getSpeciesJList() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getSpeciesJListListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getSpeciesJListListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getSpeciesList() - Method in class etomica.simulation.Simulation
-
- getSpeciesList() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSpeciesListDisplayLSM() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- getSpeciesListDisplayLSM() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getSpeciesljPotentialslist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSpeciesMembrane() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- getSpeciesMembrane() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- getSpeciesmethanePotentiallist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSpeciesMoleculeCount(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- getSpeciesMoleculeCount() - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- getSpeciesnalkanePotentiallist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSpeciespropanePotentiallist() - Static method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSpeciesRemovalMsgBox() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getSpeciesSelectedIndex() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSpeciesSelectedIndex(int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- getSpeciesSelectionDM() - Method in class etomica.virial.GUI.models.ModelAlertMsgDialog
-
- getSpeciesSolute() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- getSpeciesSolute1() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- getSpeciesSolute2() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- getSpeciesSolvent() - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- getSpeciesSolvent() - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- getSpecular() - Static method in class org.jmol.util.GData
-
- getSpecularExponent() - Static method in class org.jmol.util.GData
-
- getSpecularPercent() - Static method in class org.jmol.util.GData
-
- getSpecularPower() - Static method in class org.jmol.util.GData
-
- getSphereData(int) - Static method in class org.jmol.util.MeshSurface
-
Calculates the data (faces, vertices, normals) for a sphere.
- getSphericalInterpolationFraction(double, double, double, double) - Static method in class org.jmol.util.MeshSurface
-
- getSpinner() - Method in class etomica.graphics.DeviceSpinner
-
- getSpinnerPanel() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- getSplines() - Method in class etomica.potential.P2QChemInterpolated
-
- getSplitDisconnectedVirialGraphs(Set<Graph>) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- getSplitDisconnectedVirialGraphs(Set<Graph>) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- getSplitDisconnectedVirialGraphs(Set<Graph>) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- getSplitDisconnectedVirialGraphs(Graph) - Method in class etomica.virial.cluster.VirialDiagrams
-
- getSplitDisconnectedVirialGraphs(Graph) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- getSplitDisconnectedVirialGraphs(Graph) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- getSplitDisconnectedVirialGraphs(Set<Graph>) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- getSplitDisconnectedVirialGraphs(Set<Graph>) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) - Static method in class etomica.virial.simulations.VirialAlkaneEHTest
-
- getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) - Static method in class etomica.virial.simulations.VirialAlkaneFull
-
- getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialCH4AlkaneEHMix
-
- getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialCO2AlkaneEHMix
-
- getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialCO2AlkaneUAMix
-
- getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialCO2N2Mix
-
- getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) - Static method in class etomica.virial.simulations.VirialCO2PI
-
- getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) - Static method in class etomica.virial.simulations.VirialH2PI
-
- getSplitGraphString(Set<Graph>, VirialDiagrams, boolean) - Static method in class etomica.virial.simulations.VirialHePI
-
- getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialN2AlkaneEHMix
-
- getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialN2AlkaneUAMix
-
- getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialN2CH4Mix
-
- getSplitGraphString(Set<Graph>, VirialDiagramsMix2, boolean) - Static method in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix
-
- getSpringConstant() - Method in class etomica.modules.materialfracture.P1Tension
-
- getSpringConstant() - Method in class etomica.potential.P1Harmonic
-
- getSpringConstant() - Method in class etomica.potential.P1HarmonicSite
-
- getSpringConstant() - Method in class etomica.potential.P2Anharmonic
-
Accessor method for harmonic energy parameter
- getSpringConstant() - Method in class etomica.potential.P2Harmonic
-
Accessor method for harmonic energy parameter
- getSpringConstantDimension() - Method in class etomica.modules.materialfracture.P1Tension
-
Not implemented correctly.
- getSpringConstantDimension() - Method in class etomica.potential.P1Harmonic
-
- getSpringConstantDimension() - Method in class etomica.potential.P1HarmonicSite
-
- getSpringConstantDimension() - Method in class etomica.potential.P2Anharmonic
-
Not implemented correctly.
- getSpringConstantDimension() - Method in class etomica.potential.P2Harmonic
-
Not implemented correctly.
- getSqErr(double[], double[]) - Method in class etomica.modules.interfacial.FitTanh
-
- getSqErr(double[], double[]) - Method in class etomica.surfacetension.FitTanh
-
- getStandardPdbHydrogenCount(int) - Static method in class org.jmol.viewer.JmolConstants
-
- getStart() - Method in class g3dsys.images.Line
-
- getStartAtom() - Method in class etomica.virial.MCMoveClusterAtomMulti
-
- getState() - Method in class etomica.graphics.DeviceCheckBox
-
Returns the currents true/false state of the button.
- getState() - Method in class etomica.graphics.DeviceToggleButton
-
Returns the current true/false state of the button.
- getState() - Method in class etomica.graphics.DeviceToggleRadioButtons
-
Returns the currents true/false state of the button.
- getStaticGraphics(Object, boolean) - Method in interface org.jmol.api.ApiPlatform
-
- getStaticGraphics(Object, boolean) - Method in class org.jmol.awt.Platform
-
- getStatus() - Method in class etomica.server.representations.StatusAction
-
- getStdev() - Method in class etomica.data.AccumulatorAverageBootstrap
-
Returns the standard deviation of the block averages, for all block
sizes.
- getStdev() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Returns the standard deviation of the block averages, for all block
sizes.
- getStdevantibiasedLog() - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
-
Returns the standard deviation of the log of the block averages, for all
block sizes.
- getStdevLog() - Method in class etomica.data.AccumulatorAverageBootstrap
-
Returns the standard deviation of the log of the block averages, for all
block sizes.
- getStdevLog() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Returns the standard deviation of the log of the block averages, for all
block sizes.
- getStepCount() - Method in class etomica.integrator.Integrator
-
Returns the number of steps performed by the integrator since it was
initialized.
- getStepFreq0() - Method in class etomica.virial.overlap.IntegratorOverlap
-
- getStepSize() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- getStepSize() - Method in class etomica.integrator.mcmove.MCMoveStep
-
- getStepSize() - Method in interface etomica.integrator.mcmove.MCMoveStepDependent
-
returns the current step size.
- getStepSizeDimension() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- getStepSizeDimension() - Method in class etomica.integrator.mcmove.MCMoveStep
-
- getStepSizeMax() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- getStepSizeMax() - Method in class etomica.integrator.mcmove.MCMoveStep
-
- getStepSizeMax() - Method in interface etomica.integrator.mcmove.MCMoveStepDependent
-
Returns the maximum allowable steps size.
- getStepSizeMaxDimension() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- getStepSizeMaxDimension() - Method in class etomica.integrator.mcmove.MCMoveStep
-
- getStepSizeMin() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- getStepSizeMin() - Method in class etomica.integrator.mcmove.MCMoveStep
-
- getStepSizeMin() - Method in interface etomica.integrator.mcmove.MCMoveStepDependent
-
Returns the minimum allowable steps size.
- getStepSizeMinDimension() - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- getStepSizeMinDimension() - Method in class etomica.integrator.mcmove.MCMoveStep
-
- getStereoMode(String) - Static method in enum org.jmol.constant.EnumStereoMode
-
- getStiffness() - Method in class etomica.virial.MCMoveChangeBondLength
-
- getStiffness() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- getStockComponent(char, char) - Static method in class etomica.graph.model.impl.MetadataImpl
-
- getStore() - Method in interface etomica.graph.model.Graph
-
- getStore() - Method in class etomica.graph.model.impl.GraphImpl
-
- getStrands() - Method in class etomica.graph.property.FFTDecomposition
-
- getStrands() - Method in class etomica.graph.property.IsFFT
-
- getStreamsForSim(String) - Method in class etomica.server.resources.data.DataStreamResource
-
- getSType() - Method in class etomica.virial.Species7SiteRigidSF6
-
- getSubCluster() - Method in class etomica.virial.ClusterCoupledFlipped
-
- getSubCluster() - Method in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- getSubCluster() - Method in class etomica.virial.ClusterCoupledFlippedPartial
-
- getSubCluster() - Method in class etomica.virial.ClusterWeightAbs
-
- getSubDataInfo() - Method in class etomica.data.DataSourceGroup
-
- getSubDataInfo(int) - Method in class etomica.data.types.DataGroup.DataInfoGroup
-
Returns the DataInfo corresponding to the group's given wrapped
Data object.
- getSubDataInfo() - Method in class etomica.data.types.DataGroup.DataInfoGroupFactory
-
- getSubIntegrator() - Method in class etomica.thermointegration.IntegratorThermodynamic
-
Returns the subIntegrator, responsible for actually walking through
configurational space.
- getSulfurType() - Method in class etomica.modules.sam.SpeciesAlkaneThiol
-
- getSum() - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- getSum() - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergiesEAM
-
- getSum() - Method in class etomica.freeenergy.npath.PotentialCalculationDUDW
-
- getSum() - Method in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
-
- getSum() - Method in class etomica.meam.PotentialCalculationEnergySumEAM
-
Returns the current value of the energy sum.
- getSum() - Method in class etomica.normalmode.PotentialCalculationEFSSP
-
Returns the current value of the energy sum.
- getSum() - Method in class etomica.normalmode.PotentialCalculationLJSP
-
Returns the current value of the energy sum.
- getSum() - Method in class etomica.potential.PotentialCalculationEnergySum
-
Returns the current value of the energy sum.
- getSum() - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
Returns the current value of the energy sum.
- getSum() - Method in class etomica.potential.PotentialCalculationHyperVirialSum
-
Returns the current value of the energy sum.
- getSum() - Method in class etomica.potential.PotentialCalculationMolecularVirialSum
-
Returns the current value of the energy sum.
- getSum() - Method in class etomica.potential.PotentialCalculationPhiSum
-
Returns the current value of the energy sum.
- getSum() - Method in class etomica.potential.PotentialCalculationVirialSum
-
Returns the current value of the energy sum.
- getSum1() - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- getSum2() - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- getSum2() - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergiesEAM
-
- getSums() - Method in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
Returns the current value of the energy sum.
- getSums() - Method in class etomica.liquidLJ.PotentialCalculationSumCutoffLS
-
Returns the current value of the energy sum.
- getSurfaceArea() - Method in class etomica.math.geometry.Cube
-
Returns 6*edgeLength^2
- getSurfaceArea() - Method in class etomica.math.geometry.Cuboid
-
- getSurfaceArea() - Method in class etomica.math.geometry.Parallelepiped
-
- getSurfaceArea() - Method in class etomica.math.geometry.Polyhedron
-
Returns the sum the area of the faces of the polyhedron
- getSurfaceColor() - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
-
- getSurfaceDimension() - Method in class etomica.data.DataProcessorInterfacialTension
-
Returns the dimension of the surfaces.
- getSurfaceYOffset() - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- getSurfaceYOffset() - Method in class etomica.modules.sam.ConfigurationSAM
-
- getSweepRadius() - Method in class etomica.atom.AtomTypeSpheroPolyhedron
-
- getSwitchFac() - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- getSwitchFac() - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- getSymbol() - Method in class etomica.chem.elements.Element
-
- getSymbol() - Method in interface etomica.chem.elements.IElement
-
- getSystemSigmaHSRef() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- getT1() - Method in class etomica.normalmode.HTTPSoftSphereApplet
-
- getT2() - Method in class etomica.normalmode.HTTPSoftSphereApplet
-
- getTableModel() - Method in class etomica.graphics.DevicePlotPoints
-
- getTableUpdateInterval() - Method in class etomica.data.DataTableAverages
-
- getTag(AccumulatorAverage.StatType) - Method in class etomica.data.AccumulatorAverage
-
- getTag(AccumulatorAverageBlockless.StatType) - Method in class etomica.data.AccumulatorAverageBlockless
-
- getTag(AccumulatorAverage.StatType) - Method in class etomica.data.AccumulatorRatioAverageCovariance
-
- getTag(AccumulatorAverage.StatType) - Method in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- getTag() - Method in class etomica.data.DataDistributer
-
Returns the DataTag associated with this DataSplitter
- getTag() - Method in class etomica.data.DataDump
-
- getTag() - Method in class etomica.data.DataFork
-
- getTag() - Method in class etomica.data.DataGroupSplitter
-
Returns the DataTag associated with this DataGroupSplitter
- getTag() - Method in interface etomica.data.DataPipe
-
- getTag() - Method in class etomica.data.DataProcessor
-
- getTag() - Method in interface etomica.data.DataSourceAtomic
-
- getTag() - Method in class etomica.data.DataSourceFunction
-
- getTag() - Method in class etomica.data.DataSourceGroup
-
- getTag() - Method in interface etomica.data.DataSourceMolecular
-
- getTag() - Method in class etomica.data.DataSourcePoints
-
- getTag() - Method in interface etomica.data.DataSourcePositioned
-
- getTag() - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
-
- getTag() - Method in class etomica.data.DataSourceRmsVelocity
-
- getTag() - Method in class etomica.data.DataSourceScalar
-
- getTag() - Method in class etomica.data.DataSourceTensorVirialHard
-
- getTag() - Method in class etomica.data.DataSourceUniform
-
- getTag() - Method in class etomica.data.DataSplitter
-
Returns the DataTag associated with this DataSplitter
- getTag() - Method in class etomica.data.HistogramDataSource
-
- getTag() - Method in interface etomica.data.IDataSource
-
- getTag() - Method in class etomica.data.meter.MeterDihedralAngle
-
- getTag() - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- getTag() - Method in class etomica.data.meter.MeterHyperVirial
-
- getTag() - Method in class etomica.data.meter.MeterMomentumCOM
-
- getTag() - Method in class etomica.data.meter.MeterPositionCOM
-
- getTag() - Method in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
-
- getTag() - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
- getTag() - Method in class etomica.data.meter.MeterPressureHardTensor
-
- getTag() - Method in class etomica.data.meter.MeterPressureTensor
-
- getTag() - Method in class etomica.data.meter.MeterPressureTensorFromIntegrator
-
- getTag() - Method in class etomica.data.meter.MeterProfile
-
- getTag() - Method in class etomica.data.meter.MeterProfileByAtoms
-
- getTag() - Method in class etomica.data.meter.MeterProfileByVolume
-
- getTag() - Method in class etomica.data.meter.MeterRDF
-
- getTag() - Method in class etomica.data.meter.MeterRDFPC
-
- getTag() - Method in class etomica.data.meter.MeterStructureFactor
-
- getTag() - Method in class etomica.data.meter.MeterTensorVelocity
-
- getTag() - Method in class etomica.freeenergy.npath.DataSourceEnergies
-
- getTag() - Method in class etomica.gaussianwork.MeterBoltzmannA
-
- getTag() - Method in class etomica.gaussianwork.MeterBoltzmannB
-
- getTag() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- getTag() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- getTag() - Method in class etomica.integrator.IntegratorGear4NPH.MeterEnthalpy
-
- getTag() - Method in class etomica.integrator.IntegratorPT.BoxTracker
-
- getTag() - Method in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- getTag() - Method in class etomica.liquidLJ.MeterPU
-
- getTag() - Method in class etomica.liquidLJ.MeterPUCut
-
- getTag() - Method in class etomica.liquidLJ.MeterPUCutLS
-
- getTag() - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- getTag() - Method in class etomica.mappedRdf.MeterMappedRdf
-
- getTag() - Method in class etomica.mappedvirial.MeterMeanForce
-
- getTag() - Method in class etomica.metastable.MeterDensityDistribution
-
- getTag() - Method in class etomica.models.nitrogen.MeterBoltzmann
-
- getTag() - Method in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- getTag() - Method in class etomica.models.nitrogen.MeterNormalizedCoord
-
- getTag() - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta
-
- getTag() - Method in class etomica.models.nitrogen.MeterOrientationDistribution
-
- getTag() - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup
-
- getTag() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- getTag() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- getTag() - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
-
- getTag() - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
-
- getTag() - Method in class etomica.models.oneDHardRods.MeterOverlap
-
- getTag() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
- getTag() - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D
-
- getTag() - Method in class etomica.modules.adsorption.DataSourceDensityFunction
-
- getTag() - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- getTag() - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- getTag() - Method in class etomica.modules.droplet.MeterDeformation
-
- getTag() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- getTag() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
-
- getTag() - Method in class etomica.modules.interfacial.MeterOrientation
-
- getTag() - Method in class etomica.modules.mu.DataSourceWallPressureMu
-
- getTag() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- getTag() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- getTag() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- getTag() - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- getTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaAlpha
-
- getTag() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- getTag() - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- getTag() - Method in class etomica.modules.rosmosis.MeterFlux
-
- getTag() - Method in class etomica.modules.rosmosis.MeterOsmoticPressure
-
- getTag() - Method in class etomica.modules.sam.MeterTilt
-
- getTag() - Method in class etomica.modules.statistics.DataCollector
-
- getTag(int) - Method in class etomica.modules.statistics.DataProcessorBounds
-
- getTag() - Method in class etomica.normalmode.DataSourceFE
-
- getTag() - Method in class etomica.normalmode.DataSourceFEHistogram
-
- getTag() - Method in class etomica.normalmode.DataSourceImposedFEFit
-
- getTag() - Method in class etomica.normalmode.DataSourceImposedFEHistogram
-
- getTag() - Method in class etomica.normalmode.DataSourcePMu
-
- getTag() - Method in class etomica.normalmode.DataSourcePN
-
- getTag() - Method in class etomica.normalmode.MeterAtomicDisplacement
-
- getTag() - Method in class etomica.normalmode.MeterBoltzmann
-
- getTag() - Method in class etomica.normalmode.MeterBoltzmannHarmonic
-
- getTag() - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- getTag() - Method in class etomica.normalmode.MeterBoltzmannTarget
-
- getTag() - Method in class etomica.normalmode.MeterDADB
-
- getTag() - Method in class etomica.normalmode.MeterDDP
-
- getTag() - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- getTag() - Method in class etomica.normalmode.MeterDirectSamplingTarget
-
- getTag() - Method in class etomica.normalmode.MeterDP
-
- getTag() - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- getTag() - Method in class etomica.normalmode.MeterNormalMode
-
- getTag() - Method in class etomica.normalmode.MeterOverlapSwitch
-
- getTag() - Method in class etomica.normalmode.MeterPlaneSlip
-
- getTag() - Method in class etomica.normalmode.MeterSamplingHarmonic
-
- getTag() - Method in class etomica.normalmode.MeterSamplingTarget
-
- getTag() - Method in class etomica.normalmode.MeterSolidDA
-
- getTag() - Method in class etomica.normalmode.MeterSolidDACut
-
- getTag() - Method in class etomica.normalmode.MeterSolidMirror
-
- getTag() - Method in class etomica.normalmode.MeterSolidProps
-
- getTag() - Method in class etomica.normalmode.MeterSolidPropsLJ
-
- getTag() - Method in class etomica.normalmode.MeterTargetTP
-
- getTag() - Method in class etomica.normalmode.MeterTilt
-
- getTag() - Method in class etomica.normalmode.MeterTiltHistogram
-
- getTag() - Method in class etomica.normalmode.MeterTiltRotation
-
- getTag() - Method in class etomica.normalmode.MeterTiltRotationHistogram
-
- getTag(int) - Method in class etomica.normalmode.MeterTiltRotationHistogram
-
- getTag() - Method in class etomica.normalmode.MeterTiltRotationStdev
-
- getTag() - Method in class etomica.normalmode.MeterWorkBennetHarmonic
-
- getTag() - Method in class etomica.normalmode.MeterWorkBennetTarget
-
- getTag() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- getTag() - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- getTag() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- getTag() - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- getTag() - Method in class etomica.normalmode.MeterWorkTargetBennet
-
- getTag() - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- getTag() - Method in class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- getTag() - Method in class etomica.normalmode.MeterWorkTargetUmbrella
-
- getTag() - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- getTag() - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- getTag() - Method in class etomica.overlap.MeterOverlap
-
- getTag() - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic.LatticeEnergy
-
- getTag() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol.Lattice2ndDerivative
-
- getTag() - Method in class etomica.virial.MeterSamplingWeight
-
- getTag() - Method in class etomica.virial.MeterVirial
-
- getTag() - Method in class etomica.virial.MeterVirialBD
-
- getTag() - Method in class etomica.virial.MeterVirialBDBin
-
- getTag() - Method in class etomica.virial.MeterVirialExternalField
-
- getTag() - Method in class etomica.virial.MeterVirialExternalFieldConfined
-
- getTag() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined
-
- getTag() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
-
- getTag() - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
-
- getTag() - Method in class etomica.virial.MeterVirialExternalFieldOverlapRho
-
- getTag() - Method in class etomica.virial.MeterVirialExternalFieldRho
-
- getTag() - Method in class etomica.virial.MeterVirialExternalFieldSW
-
- getTag() - Method in class etomica.virial.MeterVirialIC
-
- getTag() - Method in class etomica.virial.MeterVirialSWWE
-
- getTags() - Method in class etomica.data.DataInfo
-
Returns the array of tags held by this DataInfo instance.
- getTags() - Method in class etomica.data.DataInfoFactory
-
- getTags() - Method in interface etomica.data.IDataInfo
-
Returns the array of tags held by this DataInfo instance.
- getTags() - Method in interface etomica.data.IDataInfoFactory
-
Returns the factory's tags as an array.
- getTargetAtom() - Method in class etomica.potential.IteratorDirective
-
- getTargetCluster() - Method in class etomica.virial.MeterVirialBDBin
-
- getTargetCluster() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- getTargetCluster() - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- getTargetCluster() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- getTargetDataInterval() - Method in class etomica.normalmode.SimOverlapModule
-
- getTargetDensity() - Method in class etomica.action.BoxInflate
-
Returns the target density of the action.
- getTargetH() - Method in class etomica.integrator.IntegratorGear4NPH
-
- getTargetHDimension() - Method in class etomica.integrator.IntegratorGear4NPH
-
- getTargetMolecule() - Method in class etomica.potential.IteratorDirective
-
- getTargetP() - Method in class etomica.integrator.IntegratorGear4NPH
-
- getTargetPDimension() - Method in class etomica.integrator.IntegratorGear4NPH
-
- getTargetSource() - Method in class etomica.overlap.DataOverlap
-
Returns object capable of retrieving data from the target system.
- getTargetT() - Method in class etomica.integrator.IntegratorGear4NPH
-
- getTargetTDimension() - Method in class etomica.integrator.IntegratorGear4NPH
-
- getTemperature() - Method in class etomica.action.AtomActionRandomizeVelocity
-
- getTemperature() - Method in class etomica.action.BoxQuench
-
Returns the quench temperature.
- getTemperature() - Method in class etomica.action.BoxRandomizeMomenta
-
- getTemperature() - Method in class etomica.action.BoxScaleMomenta
-
- getTemperature() - Method in class etomica.gaussianwork.MeterBoltzmannA
-
- getTemperature() - Method in class etomica.gaussianwork.MeterBoltzmannB
-
- getTemperature() - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- getTemperature() - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- getTemperature() - Method in class etomica.graphics.DeviceThermoSlider
-
- getTemperature() - Method in class etomica.integrator.IntegratorBox
-
- getTemperature() - Method in class etomica.integrator.IntegratorManagerMC
-
- getTemperature() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- getTemperature() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- getTemperature() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- getTemperature() - Method in class etomica.normalmode.BoltzmannProcessor
-
- getTemperature() - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
-
- getTemperature() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- getTemperature() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- getTemperature() - Method in class etomica.normalmode.MeterBoltzmannHarmonic
-
- getTemperature() - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- getTemperature() - Method in class etomica.normalmode.MeterDDP
-
- getTemperature() - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- getTemperature() - Method in class etomica.normalmode.MeterDP
-
- getTemperature() - Method in class etomica.normalmode.MeterTargetTP
-
- getTemperature() - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- getTemperature() - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- getTemperature() - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- getTemperature() - Method in class etomica.potential.P2LJDipole
-
- getTemperature() - Method in class etomica.potential.P2LJQ
-
- getTemperature() - Method in class etomica.potential.P2LJQQ
-
- getTemperature() - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
-
- getTemperature() - Method in class etomica.virial.ClusterSum
-
- getTemperature() - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- getTemperature() - Method in class etomica.virial.ClusterSumPolarizable
-
- getTemperature() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- getTemperature() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- getTemperature() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- getTemperature() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- getTemperature() - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
-
- getTemperatureDimension() - Method in class etomica.integrator.IntegratorBox
-
- getTemperatureDimension() - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
-
- getTemperatureField() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- getTemperatureSource() - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
Returns the temperature data source.
- getTetherLength() - Method in class etomica.potential.P2Tether
-
Accessor method for the tether distance
- getTetherLengthDimension() - Method in class etomica.potential.P2Tether
-
- getTextBackground() - Method in class etomica.graphics.DeviceBox
-
- getTextField() - Method in class etomica.graphics.DeviceSlider
-
- getTextPixels(String, JmolFont, Object, Object, int, int, int) - Method in interface org.jmol.api.ApiPlatform
-
- getTextPixels(String, JmolFont, Object, Object, int, int, int) - Method in class org.jmol.awt.Platform
-
- getThermostat() - Method in class etomica.integrator.IntegratorMD
-
- getThermostatInterval() - Method in class etomica.integrator.IntegratorMD
-
- getTheta() - Method in class etomica.association.BiasVolumeSphereOriented
-
- getTheta() - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
- getTheta() - Method in class etomica.models.water.P2HardAssociationGCPMReference
-
- getTheta() - Method in class etomica.models.water.PNWaterGCPMThreeSite
-
- getTheta() - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for angle describing width of cone.
- getTheta() - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for angle describing width of cone.
- getTheta() - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for angle describing width of cone.
- getTheta() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for angle describing width of cone.
- getTheta() - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for angle describing width of cone.
- getTheta() - Method in class etomica.potential.P2HardAssociationConeReference
-
Accessor method for angle describing width of cone.
- getTheta() - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
-
Accessor method for angle describing width of cone.
- getTheta() - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for angle describing width of cone.
- getTheta() - Method in class etomica.potential.P2QChemInterpolated
-
- getTheta() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getTheta() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getTheta() - Method in class org.jmol.util.Quaternion
-
- getThetaDimension() - Method in class etomica.potential.P2HardAssociationCone
-
- getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeFourSites
-
- getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
- getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeOneSite
-
- getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeReference
-
- getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
-
- getThetaDimension() - Method in class etomica.potential.P2HardAssociationConeSW
-
- getThetaDirected(Point4f) - Method in class org.jmol.util.Quaternion
-
- getThetaDirectedV(Vector3f) - Method in class org.jmol.util.Quaternion
-
- getThetaFrac() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- getThetaRadians() - Method in class org.jmol.util.Quaternion
-
- getTHigh() - Method in class etomica.graphics.ColorSchemeTemperature
-
- getThreshold() - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.AtomFilterDeviation
-
- getTilt() - Method in class etomica.math.numerical.AkimaSplineSmootherApp.PlotAction
-
- getTilt() - Method in class etomica.math.numerical.AkimaSplineSmootherDyApp.PlotAction
-
- getTimeDataSource() - Method in class etomica.data.AccumulatorHistory
-
Returns the DataSource used for the "time" component of the history.
- getTimer() - Method in class etomica.graphics.DisplayTimer
-
Returns the data source used to count the time, to permit
access to its methods for reset, etc.
- getTimeStep() - Method in class etomica.integrator.IntegratorMD
-
- getTitle() - Method in class etomica.graphics.DeviceToggleRadioButtons
-
- getTLow() - Method in class etomica.graphics.ColorSchemeTemperature
-
- getTLowDimension() - Method in class etomica.graphics.ColorSchemeTemperature
-
- getTM() - Method in class g3dsys.control.G3DSys
-
- getTokenFromName(String) - Static method in class org.jmol.script.Token
-
- getTokens(String) - Static method in class org.jmol.util.Parser
-
- getTokensAt(String, int) - Static method in class org.jmol.util.Parser
-
- getTokensLike(String) - Static method in class org.jmol.script.Token
-
- getTokFromName(String) - Static method in class org.jmol.script.Token
-
- getTolerance() - Method in class etomica.action.ActionMinimizeEnergy
-
- getTolerance() - Method in class etomica.modules.interfacial.FitTanh
-
- getTolerance() - Method in class etomica.surfacetension.FitTanh
-
- getToNode(byte) - Method in interface etomica.graph.model.Graph
-
- getToNode(byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- getToPixels() - Method in class etomica.graphics.DisplayBox
-
- getToPixels() - Method in class etomica.graphics.DisplayPolytope
-
- getTorsionpotentiala0() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getTorsionpotentiala0() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getTorsionpotentiala1() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getTorsionpotentiala1() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getTorsionpotentiala2() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getTorsionpotentiala2() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getTorsionpotentiala3() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- getTorsionpotentiala3() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- getTotalCount() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- getTotalCount() - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- getTotalCount() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- gettotcount() - Method in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- getTracker() - Method in class etomica.integrator.mcmove.MCMove
-
- getTranscoder() - Method in class etomica.graph.view.rasterizer.DestinationType
-
Returns a transcoder object of the result image type.
- getTransformationTensor() - Method in class etomica.models.nitrogen.AtomActionTransformed
-
- getTransformationTensor() - Method in class etomica.paracetamol.AtomActionTransformed
-
- getTransformedVertexVectors() - Method in class org.jmol.g3d.Graphics3D
-
- getTransformedVertexVectors() - Method in class org.jmol.util.GData
-
- getTransformMatrix4(List<Point3f>, List<Point3f>, Matrix4f, Point3f) - Static method in class org.jmol.util.Measure
-
- getTranslationVector() - Method in class etomica.action.AtomActionTranslateBy
-
Returns the translation vector, the distance that the
atom will be moved by this action.
- getTranslationVector() - Method in class etomica.action.MoleculeActionTranslateTo
-
Returns the vector that was used to accomplish the most recent translation action.
- getTrimThreshold() - Method in class etomica.atom.AtomArrayList
-
- getTrimThreshold() - Method in class etomica.molecule.MoleculeArrayList
-
- getTrueLabel() - Method in class etomica.action.ActionToggle
-
- getTrueLabel() - Method in class etomica.graphics.DeviceToggleButton
-
- getTrueLabel() - Method in class etomica.graphics.DeviceToggleRadioButtons
-
- getTruncatedPotential() - Method in class etomica.potential.Potential0Lrc
-
Returns the potential whose truncation this lrcPotential exists to correct.
- getTruncation() - Method in class etomica.potential.PotentialGroupSoft
-
- getTruncationRadius() - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
Accessor method for the radial cutoff distance.
- getTruncationRadius() - Method in class etomica.potential.P2MoleculeTruncated
-
Accessor method for the radial cutoff distance.
- getTruncationRadius() - Method in class etomica.potential.P2SoftSphericalTruncated
-
Accessor method for the radial cutoff distance.
- getTruncationRadius() - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
Accessor method for the radial cutoff distance.
- getTruncationRadius() - Method in class etomica.potential.P2SoftTruncated
-
Accessor method for the radial cutoff distance.
- getTruncationRadius() - Method in class etomica.space.BoundaryDeformablePeriodic
-
- getTruncationRadiusDimension() - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
Returns the dimension (length) of the radial cutoff distance.
- getTruncationRadiusDimension() - Method in class etomica.potential.P2MoleculeTruncated
-
Returns the dimension (length) of the radial cutoff distance.
- getTruncationRadiusDimension() - Method in class etomica.potential.P2SoftSphericalTruncated
-
Returns the dimension (length) of the radial cutoff distance.
- getTruncationRadiusDimension() - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
Returns the dimension (length) of the radial cutoff distance.
- getTruncationRadiusDimension() - Method in class etomica.potential.P2SoftTruncated
-
Returns the dimension (length) of the radial cutoff distance.
- getTSelement() - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- getTunable() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
- getType() - Method in class etomica.action.activity.ControllerEvent
-
- getType() - Method in class etomica.atom.Atom
-
- getType() - Method in interface etomica.atom.IAtom
-
- getType() - Method in interface etomica.graph.model.Edge
-
- getType() - Method in class etomica.graph.model.impl.EdgeImpl
-
- getType() - Method in class etomica.graph.model.impl.MetadataImpl
-
- getType() - Method in class etomica.graph.model.impl.NodeImpl
-
- getType() - Method in interface etomica.graph.model.Metadata
-
- getType() - Method in interface etomica.graph.model.Node
-
- getType() - Method in interface etomica.molecule.IMolecule
-
Returns the ISpecies of this IMolecule.
- getType() - Method in class etomica.molecule.Molecule
-
- getType() - Method in class etomica.nbr.CriterionType
-
Returns the AtomType accepted by this criterion.
- getTypeInteraction() - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
- getTypeMax() - Method in class etomica.data.DataSourceUniform
-
Accessor method for the type of the right limit.
- getTypeMin() - Method in class etomica.data.DataSourceUniform
-
Accessor method for the type of the left limit.
- getTypes() - Method in class etomica.nbr.CriterionTypePair
-
Returns the AtomTypes accepted by this NeighborCriterion
- getTypes() - Method in class etomica.nbr.CriterionTypesCombination
-
Returns the AtomTypes accepted by this NeighborCriterion
- getTypes() - Method in class etomica.nbr.CriterionTypesMulti
-
Returns the AtomTypes accepted by this NeighborCriterion
- getTypes() - Method in class etomica.potential.PotentialArrayByType
-
- getU123ADD(P2QChemInterpolated, double, double, double) - Method in class etomica.potential.P3AdditiveQChem
-
- getU123SCF(double, double, int) - Method in class etomica.potential.P3QChem
-
- getU_DipoleDipole() - Method in class etomica.models.water.P2WaterTIP4PHardCore
-
- getUa2(int) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
Returns average value of expression used to determine optimal
Bennet parameter (value[1]/(value[1]+expX[iParam]).
- getUDisp(double) - Method in class etomica.potential.P2QChemInterpolated
-
- getUlat0(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOS
-
- getUlat0(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- getULatFunction() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- getULatFunction() - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- getULatFunction() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- getULatFunction() - Method in class etomica.normalmode.MeterDDP
-
- getULatFunction() - Method in class etomica.normalmode.MeterDP
-
- getULatTruncFunction() - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- getULJAtDipoleCenter() - Method in class etomica.models.water.P2WaterTIP4PHardCore
-
- getUnit() - Method in class etomica.graphics.Device
-
- getUnit() - Method in class etomica.graphics.DimensionedDoubleEditor
-
- getUnit() - Method in class etomica.graphics.DisplayScrollingGraph
-
Returns the physical units of the displayed value.
- getUnit(int) - Method in class etomica.graphics.DisplayTable
-
Returns the unit assign to the i-th column (as defined before any
transpose).
- getUnit() - Method in class etomica.graphics.DisplayTextBox
-
Returns the physical units of the displayed value.
- getUnit() - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Angle
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Area
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Charge
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.CompoundDimension
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Current
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Dimension
-
Returns the unit of this dimension as derived in the given system of units.
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.DimensionRatio
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Dipole
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.ElectricPotential
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Energy
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Force
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Fraction
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Frequency
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Length
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.LuminousIntensity
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Mass
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Momentum
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Null
-
Returns UNIT, regardless of the given unit system.
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Power
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Pressure
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Pressure2D
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Quantity
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Temperature
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Time
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Undefined
-
Returns UNIT, regardless of the given unit system.
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Velocity
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Viscosity
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Volume
-
- getUnit(UnitSystem) - Method in class etomica.units.dimensions.Wavenumber
-
- getUnitVectors(double[][], Vector3f[], float[]) - Static method in class org.jmol.util.Eigen
-
- getUnscreenedCount() - Method in class etomica.virial.MeterVirialBDBin
-
- getUpdatedDimensions() - Method in class etomica.zeolite.ConfigurationFileXYZ
-
- getUpdateInterval() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
Returns the interval for which neighbor update checks are performed.
- getUpdateInterval() - Method in class etomica.nbr.list.NeighborListManager
-
Returns the interval for which neighbor update checks are performed.
- getUpList() - Method in class etomica.nbr.list.AtomNeighborLists
-
Returns an array of uplist-neighbor-atom lists.
- getUpList() - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists
-
Returns an array of uplist-neighbor-molecule lists.
- getUpList(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- getUpList(IAtom) - Method in class etomica.nbr.list.NeighborListManager
-
- getUpperLimit() - Method in class etomica.models.hexane.SpeciesHexane
-
- getUpsilon(int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOS
-
- getUpsilon(int, double, double) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- getuReactCO() - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- getuReactCORev() - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- getURI() - Method in class etomica.graph.view.rasterizer.SVGConverterDocumentSource
-
- getURI() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
-
- getURI() - Method in interface etomica.graph.view.rasterizer.SVGConverterSource
-
Returns a URI string corresponding to this source
- getURI() - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
-
- getUSCF(double) - Method in class etomica.potential.P2QChemInterpolated
-
- getUserStylesheet() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getUseSurfaceOnly() - Method in class etomica.modules.droplet.P2Cohesion
-
- getUSums() - Method in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
Returns the current value of the energy sum.
- getV() - Method in class etomica.eigenstuff.MyEigenvalueDecomposition
-
Return the eigenvector matrix
- getV1() - Method in class etomica.models.hexane.ConformationHexane
-
- getV2() - Method in class etomica.models.hexane.ConformationHexane
-
- getVacancyFraction(double) - Method in class etomica.statmech.HardSphereSolid
-
Returns the fraction of lattice sites with a vacancy for the given
lattice density.
- getVacancyFreeEnergy(double) - Method in class etomica.statmech.HardSphereSolid
-
Returns the Helmholtz free energy difference due to the presence of
vacancies at the given lattice density.
- getVacancyPressure(double) - Method in class etomica.statmech.HardSphereSolid
-
Returns the difference between the pressure with vacancies from the
pressure without vacancies for the given lattice density.
- getValidate() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getValue(int, int) - Method in class etomica.data.DataSinkTable
-
- getValue(int) - Method in interface etomica.data.IData
-
Returns the i-th data value.
- getValue(int) - Method in class etomica.data.types.DataDouble
-
Returns this instance's value if argument is 0, otherwise throw exception
- getValue(int) - Method in class etomica.data.types.DataDoubleArray
-
Returns the i-th value of the wrapped array.
- getValue(int[]) - Method in class etomica.data.types.DataDoubleArray
-
Returns the element of the array indicated by the given set of indices.
- getValue(int) - Method in class etomica.data.types.DataDoubleBDArray
-
Returns the i-th value of the wrapped array.
- getValue(int[]) - Method in class etomica.data.types.DataDoubleBDArray
-
Returns the element of the array indicated by the given set of indices.
- getValue(int) - Method in class etomica.data.types.DataGroup
-
- getValue(int) - Method in class etomica.data.types.DataTable
-
Returns the i-th data value, where the values are numbered by counting down the first column,
then the next, and so on.
- getValue(int) - Method in class etomica.data.types.DataTensor
-
Returns the i-th tensor value, indexing across the first row, then the
second, etc.
- getValue(int) - Method in class etomica.data.types.DataVector
-
Returns the i-th vector value.
- getValue() - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- getValue() - Method in class etomica.graph.engine.impl.CommandPropertyValueImpl
-
- getValue() - Method in class etomica.graph.engine.impl.CommandValueImpl
-
- getValue() - Method in class etomica.graph.engine.impl.CommandVariableValueImpl
-
- getValue() - Method in class etomica.graph.engine.impl.ValueImpl
-
- getValue() - Method in interface etomica.graph.engine.Parser.CommandPropertyValue
-
- getValue() - Method in interface etomica.graph.engine.Parser.CommandValue
-
- getValue() - Method in interface etomica.graph.engine.Parser.CommandVariableValue
-
- getValue() - Method in interface etomica.graph.engine.Parser.Value
-
- getValue() - Method in interface etomica.graph.model.Coefficient
-
- getValue() - Method in class etomica.graph.model.impl.CoefficientImpl
-
- getValue() - Method in class etomica.graphics.DeviceBoxValueChangedEvent
-
- getValue() - Method in class etomica.graphics.DeviceSlider
-
- getValue() - Method in class etomica.graphics.DeviceSpinner
-
- getValue() - Method in class etomica.graphics.DimensionedDoubleEditor
-
Returns the value in simulation units.
- getValue() - Method in class etomica.liquidLJ.LjMd3D.ValueCache
-
- getValue() - Method in class etomica.liquidLJ.ValueCache
-
- getValue() - Method in interface etomica.modifier.Modifier
-
Gets the current value of the property.
- getValue() - Method in class etomica.modifier.ModifierFunctionWrapper
-
Applies inverse of function to property before returning it.
- getValue() - Method in class etomica.modifier.ModifierGeneral
-
- getValue() - Method in class etomica.modifier.ModifierNMolecule
-
- getValue() - Method in class etomica.modifier.ModifyAction
-
- getValue() - Method in class etomica.modules.adsorption.ModifierPMu
-
- getValue() - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
-
- getValue() - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
-
- getValue() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
-
- getValue() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
-
- getValue() - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- getValue() - Method in class etomica.modules.entropylottery.ModifierDimensions
-
- getValue() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- getValue() - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- getValue() - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- getValue() - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- getValue() - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
-
- getValue() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
-
- getValue() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
-
- getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
-
- getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
-
- getValue() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- getValue() - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
-
- getValue() - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
-
- getValue() - Method in class etomica.normalmode.ModifierCells3D
-
- getValue() - Method in class etomica.normalmode.ModifierXCells2D
-
- getValue() - Method in class etomica.normalmode.ModifierYCells2D
-
- getValue(String) - Method in class etomica.util.Grabber.ActionCornerSetter
-
- getValue() - Method in class etomica.virial.simulations.ModifierTPI
-
- getValueAt(int, int) - Method in class etomica.graphics.DeviceTableModelGeneric
-
Get the value in the given table cell.
- getValueAt(int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- getValueAt(int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- getValueAt(int, int) - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- getValueProperties() - Method in class etomica.meta.wrappers.Wrapper
-
- getValues() - Method in class etomica.graph.view.rasterizer.DestinationType
-
Defines valid image types.
- getValues() - Method in class etomica.meta.wrappers.Wrapper
-
- getValueString(Field) - Method in class etomica.util.ParameterBase
-
Actually writes field name and value to a file using fileWriter.
- getValueString(Object, Field) - Method in interface etomica.util.ParameterParser
-
Returns the value of obj's field as a string if this parser is
appropirate for the given field, or throws an exception if it's not.
- getVanderwaalsMar(int, EnumVdw) - Static method in class org.jmol.util.Elements
-
- getVaporColor() - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- getVar(MathContext) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- getVar() - Method in class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- getVar(int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- getVarDouble() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- getVariable() - Method in class etomica.graph.engine.impl.AssignmentImpl
-
- getVariable() - Method in class etomica.graph.engine.impl.CommandVariableImpl
-
- getVariable() - Method in class etomica.graph.engine.impl.CommandVariableValueImpl
-
- getVariable() - Method in interface etomica.graph.engine.Parser.Assignment
-
- getVariable() - Method in interface etomica.graph.engine.Parser.CommandVariable
-
- getVariable() - Method in interface etomica.graph.engine.Parser.CommandVariableValue
-
- getVariable(Object) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableAD(double[]) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableAF(float[]) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableAFF(float[][]) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableAI(int[]) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableAII(int[][]) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableAP(Point3f[]) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableAS(String[]) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableAV(ScriptVariable[]) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableList(List<?>) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableMap(Object) - Static method in class org.jmol.script.ScriptVariable
-
- getVariableNames() - Method in interface etomica.graph.engine.Environment
-
- getVariableNames() - Method in class etomica.graph.engine.impl.EnvironmentImpl
-
- getVariableValue(String) - Method in interface etomica.graph.engine.Environment
-
- getVariableValue(String) - Method in class etomica.graph.engine.impl.EnvironmentImpl
-
- getVdwLabel() - Method in enum org.jmol.constant.EnumVdw
-
- getVdwType(String) - Static method in enum org.jmol.constant.EnumVdw
-
- getVdwType2(String) - Static method in enum org.jmol.constant.EnumVdw
-
- getVector() - Method in class etomica.math.Quaternion
-
Returns the vector part of the Quaternion as Vector
- getVector(int) - Method in class org.jmol.util.Quaternion
-
- getVectorAsDoubleArray() - Method in class etomica.math.Quaternion
-
Returns the vector associated with the Quaternion as a double array
- getVectorMagnitude() - Method in class etomica.math.Quaternion
-
Returns the magnitude of the vector associated with the Quaternion
- getVectorScale() - Method in class etomica.action.BoxInflate
-
Returns the current value of the inflation scale in each dimension.
- getVectorsFromFile(String) - Static method in class etomica.math.numerical.ArrayReader1D
-
- getVectorsFromFile(String) - Static method in class etomica.normalmode.ArrayReader1D
-
- getVelocity() - Method in class etomica.atom.AtomLeafDynamic
-
- getVelocity() - Method in interface etomica.atom.IAtomKinetic
-
- getVelocity() - Method in interface etomica.molecule.IMoleculeKinetic
-
- getVelocity() - Method in class etomica.molecule.MoleculeOrientedDynamic
-
- getVelocityAverage(IMolecule) - Method in class etomica.atom.AtomGroupVelocityAverage
-
Returns the mass-average velocity of the given Atom and
all its children.
- getVertex1() - Method in class g3dsys.images.Triangle
-
- getVertex2() - Method in class g3dsys.images.Triangle
-
- getVertex3() - Method in class g3dsys.images.Triangle
-
- getVertexCount() - Method in class etomica.math.geometry.Polytope
-
Number of vertices in the polytrope.
- getVertexCount(int) - Static method in class org.jmol.util.Geodesic
-
- getVertexVector(int) - Static method in class org.jmol.util.Geodesic
-
- getVertexVectors() - Static method in class org.jmol.util.Geodesic
-
- getVertexVectors() - Static method in class org.jmol.util.Normix
-
- getVertGBC() - Static method in class etomica.graphics.SimulationPanel
-
- getVertices() - Method in class etomica.atom.AtomTypeSpheroPolyhedron
-
- getVertices() - Method in class etomica.math.geometry.LineSegment
-
- getVertices() - Method in class etomica.math.geometry.Polytope
-
Returns an array of all vertices of the polytrope.
- getVertices() - Method in class org.jmol.util.MeshSurface
-
- getVib0(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOS
-
- getVib0(int, int) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- getViewSpeciesSelection() - Method in class etomica.virial.GUI.views.AppViewMixtureBuilder
-
- getVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- getVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- getVirialGraphs() - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- getVirialGraphs() - Method in class etomica.virial.cluster.VirialDiagrams
-
- getVirialGraphs() - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- getVirialGraphs() - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- getVirialGraphs() - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- getVirialProfile() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
Current value of the meter, obtained by dividing sum of collision virial contributions by time elapsed since last call.
- getVirialSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- getVirialSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- getVMax() - Method in class etomica.graphics.DisplayScrollingGraph
-
- getVMin() - Method in class etomica.graphics.DisplayScrollingGraph
-
- getVolume() - Method in class etomica.math.geometry.Circle
-
Returns the volume for the present sphere radius.
- getVolume() - Method in class etomica.math.geometry.Cube
-
Returns edgeLength^3.
- getVolume() - Method in class etomica.math.geometry.Cuboid
-
- getVolume() - Method in class etomica.math.geometry.Hypersphere
-
- getVolume() - Method in class etomica.math.geometry.LineSegment
-
- getVolume() - Method in class etomica.math.geometry.Parallelepiped
-
Calculated parallelepiped volume using (a X b) .
- getVolume() - Method in class etomica.math.geometry.Point
-
Returns zero.
- getVolume() - Method in class etomica.math.geometry.Polygon
-
Returns the 2-D volume of the polygon, which is its area
- getVolume() - Method in class etomica.math.geometry.PolyhedronGeneral
-
Returns the 3-D volume of the polyhedron, which is its conventional volume
- getVolume() - Method in class etomica.math.geometry.Polytope
-
Returns the (hyper)volume enclosed by the polytope.
- getVolume() - Method in interface etomica.math.geometry.Shape
-
Returns the (hyper-)volume of the enclosed region.
- getVolume() - Method in class etomica.math.geometry.Sphere
-
Returns the volume for the present sphere radius.
- getVolume() - Method in class etomica.math.geometry.TruncatedOctahedron
-
- getVSums() - Method in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
Returns the current value of the energy sum.
- getVZero() - Method in class etomica.yukawa.P2Yukawa
-
- getW() - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- getW(int) - Method in class etomica.virial.cluster.ClusterOperations
-
Returns all diagrams of order n in the sum [eta(r) + b(r)] (i.e., the sum of the indirect correlation
function and the bridge function).
- getWallDim() - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
- getWallDim() - Method in class etomica.modules.sam.P1WCAWall
-
- getWallForce() - Method in interface etomica.modules.rosmosis.IPotentialCalculationWallForce
-
- getWallForce() - Method in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
-
- getWallForce() - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
- getWallForce() - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
-
- getWallPosition() - Method in class etomica.modules.sam.P1WCAWall
-
- getWallPosition() - Method in class etomica.nbr.CriterionPositionWall
-
Returns the position of the wall.
- getWallPosition() - Method in class etomica.potential.P1HardMovingBoundary
-
- getWallPositionDimension() - Method in class etomica.nbr.CriterionPositionWall
-
- getWallPositionDimension() - Method in class etomica.potential.P1HardMovingBoundary
-
- getWallPotential() - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
-
- getWallVelocity() - Method in class etomica.potential.P1HardMovingBoundary
-
- getWallVelocityDimension() - Method in class etomica.potential.P1HardMovingBoundary
-
- getWaveVectorFactory() - Method in class etomica.normalmode.CalcJacobian
-
- getWaveVectorFactory() - Method in class etomica.normalmode.LatticeSumMolecularCrystal
-
- getWaveVectorFactory() - Method in class etomica.normalmode.MeterNormalMode
-
- getWaveVectorFactory() - Method in interface etomica.normalmode.NormalModes
-
Returns a factory that provides the wave vectors and coefficients for
the periodic system.
- getWaveVectorFactory() - Method in class etomica.normalmode.NormalModes1DHR
-
- getWaveVectorFactory() - Method in class etomica.normalmode.NormalModes2D
-
- getWaveVectorFactory() - Method in class etomica.normalmode.NormalModes3D
-
- getWaveVectorFactory() - Method in class etomica.normalmode.NormalModesFromFile
-
- getWaveVectorFactory() - Method in class etomica.normalmode.NormalModesMolecular
-
- getWaveVectorFactory() - Method in class etomica.normalmode.NormalModesPotential
-
- getWaveVectorFactory() - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- getWaveVectorFactory() - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- getWaveVectorNum() - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
- getWaveVectorNum() - Method in class etomica.normalmode.IntegratorHarmonic
-
- getWaveVectors() - Method in class etomica.normalmode.IntegratorHarmonic
-
- getWaveVectors() - Method in class etomica.normalmode.MeterNormalMode
-
- getWaveVectors() - Method in class etomica.normalmode.NormalModesVariable
-
- getWaveVectors() - Method in interface etomica.normalmode.WaveVectorFactory
-
Returns the wave vectors generated by makeWaveVectors
- getWaveVectors() - Method in class etomica.normalmode.WaveVectorFactory1D
-
- getWaveVectors() - Method in class etomica.normalmode.WaveVectorFactory2D
-
- getWaveVectors() - Method in class etomica.normalmode.WaveVectorFactoryFcc
-
- getWaveVectors() - Method in class etomica.normalmode.WaveVectorFactoryFromFile
-
- getWaveVectors() - Method in class etomica.normalmode.WaveVectorFactorySimple
-
- getWeight() - Method in class etomica.virial.cluster.ClusterDiagram
-
- getWeightCoefficients() - Method in class etomica.virial.ClusterWeightUmbrella
-
- getWeights() - Method in class etomica.virial.ClusterSum
-
- getWeightUpdateInterval() - Method in class etomica.tmmc.IntegratorTMMC
-
Accessor method for number of doStep calls between updating of weights.
- getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for attractive-well diameter divided by sigma
- getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for attractive-well diameter divided by sigma
- getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for attractive-well diameter divided by sigma
- getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for attractive-well diameter divided by sigma
- getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for attractive-well diameter divided by sigma
- getWellCutoffFactor() - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for attractive-well diameter divided by sigma
- getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationCone
-
- getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSites
-
- getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
- getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationConeOneSite
-
- getWellCutoffFactorDimension() - Static method in class etomica.potential.P2HardAssociationConeSW
-
- getWellDiameter() - Method in class etomica.potential.P2HardAssociation
-
Accessor for well diameter.
- getWellDiameterDimension() - Method in class etomica.potential.P2HardAssociation
-
- getWellEdgeCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- getWellEpsilon() - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for attractive-well depth parameter.
- getWellEpsilon() - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for attractive-well depth parameter.
- getWellEpsilon() - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for attractive-well depth parameter.
- getWellEpsilon() - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for attractive-well depth parameter.
- getWellEpsilon() - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for attractive-well depth parameter.
- getWellEpsilon() - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for attractive-well depth parameter.
- getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationCone
-
- getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSites
-
- getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
- getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeOneSite
-
- getWellEpsilonDimension() - Static method in class etomica.potential.P2HardAssociationConeSW
-
- getWidth() - Method in class etomica.graph.view.rasterizer.SVGConverter
-
- getWindow(Container) - Static method in class org.jmol.awt.Platform
-
- getWrapped() - Method in class etomica.meta.wrappers.Wrapper
-
- getWrappedClass() - Method in class etomica.meta.wrappers.Wrapper
-
- getWrappedCriterion() - Method in class etomica.nbr.CriterionAdapter
-
Returns the criterion wrapped by this adapter
- getWrappedCriterion() - Method in class etomica.nbr.molecule.CriterionAdapterMolecular
-
Returns the criterion wrapped by this adapter
- getWrappedId() - Method in class etomica.meta.wrappers.Wrapper
-
- getWrappedModifier() - Method in class etomica.modifier.ModifyAction
-
- getWrappedModifier() - Method in class etomica.modifier.ModifyBooleanAction
-
- getWrappedPotential() - Method in class etomica.normalmode.P2XOrder
-
- getWrappedPotential() - Method in class etomica.potential.P2HardWrapper
-
- getWrappedPotential() - Method in class etomica.potential.P2MoleculeMonatomic
-
- getWrappedPotential() - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
Returns the wrapped potential.
- getWrappedPotential() - Method in class etomica.potential.P2MoleculeTruncated
-
Returns the wrapped potential.
- getWrappedPotential() - Method in class etomica.potential.P2SoftSphericalTruncated
-
Returns the wrapped potential.
- getWrappedPotential() - Method in class etomica.potential.P2SoftSphericalTruncatedShifted
-
Returns the wrapped potential.
- getWrappedPotential() - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
Returns the wrapped potential.
- getWrappedPotential() - Method in class etomica.potential.P2SoftTruncated
-
Returns the wrapped potential.
- getWrappedRandom() - Method in class etomica.util.random.RandomNumberGenerator
-
- getWrapper(Object) - Method in class etomica.meta.SimulationModel
-
- getWrapper(Object, SimulationModel) - Static method in class etomica.meta.WrapperIndex
-
- getWrapperById(long) - Method in class etomica.meta.SimulationModel
-
- getWrapperClass(String) - Method in class etomica.util.ReadParameters
-
- getWriteInterval() - Method in class etomica.data.DataLogger
-
- getWriteOnFinishDataSource() - Method in class etomica.data.DataLogger
-
- getWriteScale() - Method in class etomica.graphics.DisplayCanvas
-
- getWriteVelocity() - Method in class etomica.action.WriteConfigurationDLPOLY
-
- getWriteVelocity() - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
- getX(int) - Method in interface etomica.space.Vector
-
Vector components corresponding to the given index.
- getX(int) - Method in class etomica.space1d.Vector1D
-
- getX(int) - Method in class etomica.space2d.Vector2D
-
- getX(int) - Method in class etomica.space3d.Vector3D
-
- getX(int) - Method in class etomica.spaceNd.VectorND
-
- getX() - Method in class g3dsys.images.Ball
-
- getX() - Method in class g3dsys.images.Ellipse
-
- getX0() - Method in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- getX0() - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- getX0() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- getX0() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- getX0() - Method in class etomica.potential.P1Harmonic
-
- getX0Dimension() - Method in class etomica.potential.P1Harmonic
-
- getXCellModifier() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- getXCellNum() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- getXDataSource() - Method in class etomica.data.meter.MeterDihedralAngle
-
- getXDataSource() - Method in class etomica.data.meter.MeterProfileByVolume
-
- getXDataSource() - Method in class etomica.data.meter.MeterRDF
-
- getXDataSource() - Method in class etomica.data.meter.MeterRDFPC
-
- getXDataSource() - Method in class etomica.data.meter.PotentialCalculationRDF
-
- getXDataSource() - Method in class etomica.data.types.DataFunction.DataInfoFunction
-
- getXDataSource() - Method in class etomica.data.types.DataFunction.DataInfoFunctionFactory
-
Returns a copy of array of independent DataInfo.
- getXDataSource() - Method in class etomica.mappedRdf.MeterMappedRdf
-
- getXMax() - Method in class etomica.data.DataSourceUniform
-
Accessor method for the right limit of the range.
- getXMin() - Method in class etomica.data.DataSourceUniform
-
Accessor method for the left limit of the range.
- getXRange() - Method in interface etomica.data.histogram.Histogram
-
Returns the range of x values (min and max) used in the histogram.
- getXRange() - Method in class etomica.data.histogram.HistogramDiscrete
-
- getXRange() - Method in class etomica.data.histogram.HistogramNotSoSimple
-
- getXRange() - Method in class etomica.data.histogram.HistogramReweightedData
-
- getXRange() - Method in class etomica.data.histogram.HistogramSimple
-
- getXRot() - Method in class etomica.graphics.DisplayCanvas
-
- getXSource() - Method in class etomica.data.DataSourceFunction
-
Returns the DataSourceUniform instance that generates the x values.
- getXType() - Method in class etomica.models.rowley.SpeciesEthanol
-
- getXType() - Method in class etomica.models.rowley.SpeciesMethanol
-
- getXValues() - Method in interface etomica.data.history.History
-
Returns an array containing the x values that have been added to the
History.
- getXValues() - Method in class etomica.data.history.HistoryCollapsing
-
- getXValues() - Method in class etomica.data.history.HistoryComplete
-
- getXValues() - Method in class etomica.data.history.HistoryScrolling
-
- getXValues() - Method in class etomica.modules.statistics.HistoryStatistics
-
- getXzOrientationTensor() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- getY() - Method in class g3dsys.images.Ball
-
- getY() - Method in class g3dsys.images.Ellipse
-
- getYCellModifier() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- getYCellNum() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- getYesButton() - Method in class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
-
- getyOrientationTensor() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- getYRot() - Method in class etomica.graphics.DisplayCanvas
-
- getYScale() - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
- getZ() - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- getZ() - Method in class g3dsys.images.Ball
-
- getZ() - Method in class g3dsys.images.Ellipse
-
- getZ1() - Method in class etomica.potential.P2ModifiedMorse
-
- getZ2() - Method in class etomica.potential.P2ModifiedMorse
-
- getZero() - Method in class etomica.veos.BigValue
-
- getZero() - Method in interface etomica.veos.IBigValue
-
Returns an instance of the class representing the value zero.
- getZero() - Method in class etomica.veos.MyBigDecimal
-
- getZFraction() - Method in class etomica.modules.adsorption.MyMCMove
-
- getZFraction() - Method in class etomica.modules.dcvgcmd.MyMCMove
-
Returns the zFraction.
- getZoom() - Method in class etomica.graphics.DisplayCanvas
-
- ghostBox - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- ghostBox - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- ghostBox - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- gi - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- gi - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- gi - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- gi - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- gjke(AtomOrientedQuaternion, AtomOrientedQuaternion) - Method in class etomica.potential.P2SpheroPolyhedron
-
- globalAtomLeafIndexChanged(int) - Method in class etomica.box.BoxEventManager
-
- GlobalFilter - Class in etomica.graph.iterators.filters
-
A GlobalFilter is one that must see the entire graph stream before returning any graph.
- GlobalFilter(GraphIterator) - Constructor for class etomica.graph.iterators.filters.GlobalFilter
-
- GlobalFilter(GraphIterator, GlobalFilter.SignatureMaker) - Constructor for class etomica.graph.iterators.filters.GlobalFilter
-
- GlobalFilter.SignatureMaker - Class in etomica.graph.iterators.filters
-
- globalMoveProbability - Variable in class etomica.integrator.IntegratorManagerMC
-
- go() - Method in class etomica.math.numerical.AkimaSplineSmootherApp
-
- go() - Method in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- goButton - Variable in class etomica.modules.clustergenerator.MyApplet
-
- goFastButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- GOLD - Static variable in class org.jmol.util.Colix
-
- Gperp - Variable in class etomica.dimer.IntegratorDimerRT
-
- Gperplast - Variable in class etomica.dimer.IntegratorDimerRT
-
- Gpol - Variable in class etomica.models.water.P2WaterSzalewicz
-
- Grabber - Class in etomica.util
-
- Grabber(String) - Constructor for class etomica.util.Grabber
-
- grabber - Variable in class etomica.util.Grabber.ActionCornerSetter
-
- grabber - Variable in class etomica.util.Grabber.CornerSetListener
-
- grabber - Variable in class etomica.util.Grabber.DefaultMouseListener
-
- Grabber.ActionCornerSetter - Class in etomica.util
-
- Grabber.CornerData - Class in etomica.util
-
- Grabber.CornerSetListener - Class in etomica.util
-
- Grabber.DefaultMouseListener - Class in etomica.util
-
- Grabber.ImagePanel - Class in etomica.util
-
- grabPixels(Object, int, int, int[], int, int) - Method in interface org.jmol.api.ApiPlatform
-
- grabPixels(Object, int, int, int[], int, int) - Method in class org.jmol.awt.Platform
-
- grad - Variable in class etomica.interfacial.P1Wall
-
- gradient(IAtomList) - Method in class etomica.dimer.P1LepsHarmonic
-
- gradient(IAtomList, Tensor) - Method in class etomica.dimer.P1LepsHarmonic
-
- gradient - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
-
- gradient(IAtomList) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- gradient(IAtomList, Tensor) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- gradient(IAtomList) - Method in class etomica.interfacial.P1Wall
-
- gradient(IAtomList, Tensor) - Method in class etomica.interfacial.P1Wall
-
- gradient - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- gradient(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
Gradient of the pair potential as given by the du(double) method.
- gradient(IAtomList, Tensor) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- gradient - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- gradient(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
Gradient of the pair potential as given by the du(double) method.
- gradient(IAtomList, Tensor) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- gradient - Variable in class etomica.meam.P2EAM
-
- gradient(IAtomList) - Method in class etomica.meam.P2EAM
-
- gradient(IAtomList, Tensor) - Method in class etomica.meam.P2EAM
-
- gradient - Variable in class etomica.meam.PotentialCuLREP
-
- gradient(IAtomList) - Method in class etomica.meam.PotentialCuLREP
-
- gradient(IAtomList, Tensor) - Method in class etomica.meam.PotentialCuLREP
-
- gradient - Variable in class etomica.meam.PotentialEAM
-
- gradient(IAtomList) - Method in class etomica.meam.PotentialEAM
-
- gradient(IAtomList, Tensor) - Method in class etomica.meam.PotentialEAM
-
- gradient - Variable in class etomica.meam.PotentialEAM_LS
-
- gradient(IAtomList) - Method in class etomica.meam.PotentialEAM_LS
-
- gradient(IAtomList, Tensor) - Method in class etomica.meam.PotentialEAM_LS
-
- gradient - Variable in class etomica.meam.PotentialEFS
-
- gradient(IAtomList) - Method in class etomica.meam.PotentialEFS
-
- gradient(IAtomList, Tensor) - Method in class etomica.meam.PotentialEFS
-
- gradient(IAtomList) - Method in class etomica.meam.PotentialMEAM
-
- gradient(IAtomList, Tensor) - Method in class etomica.meam.PotentialMEAM
-
- gradient(IAtomList) - Method in class etomica.models.co2.P2CO2H2OWheatley
-
- gradient(IAtomList, Tensor) - Method in class etomica.models.co2.P2CO2H2OWheatley
-
- gradient(IAtomList) - Method in class etomica.models.co2.P2CO2Hellmann
-
- gradient(IAtomList, Tensor) - Method in class etomica.models.co2.P2CO2Hellmann
-
- gradient - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- gradient(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- gradient - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- gradient(IMoleculeList) - Method in class etomica.models.nitrogen.P2NitrogenAB
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.models.nitrogen.P2NitrogenAB
-
- gradient - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- gradient(IMoleculeList) - Method in class etomica.models.nitrogen.P2NitrogenShellModel
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.models.nitrogen.P2NitrogenShellModel
-
- gradient - Variable in class etomica.models.water.P2Water3PSoft
-
- gradient(IMoleculeList) - Method in class etomica.models.water.P2Water3PSoft
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.models.water.P2Water3PSoft
-
- gradient - Variable in class etomica.models.water.P2Water4PSoft
-
- gradient(IMoleculeList) - Method in class etomica.models.water.P2Water4PSoft
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.models.water.P2Water4PSoft
-
- gradient(IAtomList) - Method in class etomica.models.water.P2WaterSzalewicz
-
- gradient(IAtomList, Tensor) - Method in class etomica.models.water.P2WaterSzalewicz
-
- gradient(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- gradient(IAtomList, Tensor) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- gradient - Variable in class etomica.modules.dcvgcmd.P1WCAWall
-
- gradient(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
- gradient(IAtomList, Tensor) - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
- gradient - Variable in class etomica.modules.droplet.P1Smash
-
- gradient(IAtomList, Tensor) - Method in class etomica.modules.droplet.P1Smash
-
- gradient(IAtomList) - Method in class etomica.modules.droplet.P1Smash
-
- gradient(IAtomList, Tensor) - Method in class etomica.modules.droplet.P2Cohesion
-
- gradient(IAtomList) - Method in class etomica.modules.droplet.P2Cohesion
-
- gradient(IAtomList, Tensor) - Method in class etomica.modules.materialfracture.P1Tension
-
- gradient(IAtomList) - Method in class etomica.modules.materialfracture.P1Tension
-
- gradient - Variable in class etomica.modules.rosmosis.P1Tether
-
- gradient(IAtomList) - Method in class etomica.modules.rosmosis.P1Tether
-
- gradient(IAtomList, Tensor) - Method in class etomica.modules.rosmosis.P1Tether
-
- gradient - Variable in class etomica.modules.sam.P1Sinusoidal
-
- gradient(IAtomList) - Method in class etomica.modules.sam.P1Sinusoidal
-
- gradient(IAtomList, Tensor) - Method in class etomica.modules.sam.P1Sinusoidal
-
- gradient - Variable in class etomica.modules.sam.P1WCAWall
-
- gradient(IAtomList) - Method in class etomica.modules.sam.P1WCAWall
-
- gradient(IAtomList, Tensor) - Method in class etomica.modules.sam.P1WCAWall
-
- gradient(IAtomList) - Method in class etomica.paracetamol.P2ElectrostaticDreiding
-
- gradient - Variable in class etomica.potential.EwaldSummation
-
- gradient(IAtomList) - Method in class etomica.potential.EwaldSummation
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.EwaldSummation
-
- gradient(IAtomList) - Method in class etomica.potential.EwaldSummation.P2EwaldReal
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.EwaldSummation.P2EwaldReal
-
- gradient(IAtomList) - Method in class etomica.potential.P1Harmonic
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P1Harmonic
-
- gradient(IAtomList) - Method in class etomica.potential.P1HarmonicSite
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P1HarmonicSite
-
- gradient(IAtomList) - Method in class etomica.potential.P1SoftBoundary
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P1SoftBoundary
-
- gradient(IAtomList) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- gradient(IAtomList) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
- gradient(IAtomList) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2HSDipole
-
- gradient(IMoleculeList) - Method in class etomica.potential.P2HSDipole
-
- gradient(IAtomList) - Method in class etomica.potential.P2Ideal
-
Returns a zero vector.
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P2Ideal
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2LJDipole
-
- gradient(IMoleculeList) - Method in class etomica.potential.P2LJDipole
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P2LJQ
-
- gradient(IAtomList) - Method in class etomica.potential.P2LJQ
-
- gradient(IMoleculeList) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- gradient(IAtomList) - Method in class etomica.potential.P2NitrogenHellmann
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P2NitrogenHellmann
-
- gradient(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2ReactionFieldDipole
-
- gradient(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- gradient - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- gradient(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- gradient(IAtomList) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
-
- gradient - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- gradient(IAtomList) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- gradient - Variable in class etomica.potential.P2SoftTruncated
-
- gradient(IAtomList) - Method in class etomica.potential.P2SoftTruncated
-
Returns the derivative (r du/dr) of the wrapped potential if the separation
is less than the cutoff value
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P2SoftTruncated
-
Returns the derivative (r du/dr) of the wrapped potential if the separation
is less than the cutoff value
- gradient - Variable in class etomica.potential.P3BondAngle
-
- gradient(IAtomList) - Method in class etomica.potential.P3BondAngle
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P3BondAngle
-
- gradient - Variable in class etomica.potential.P3BondAngleDreiding
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P3BondAngleDreiding
-
- gradient(IAtomList) - Method in class etomica.potential.P3BondAngleDreiding
-
- gradient - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- gradient(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- gradient - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- gradient(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- gradient - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- gradient(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- gradient - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- gradient(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- gradient - Variable in class etomica.potential.P4BondTorsion
-
- gradient(IAtomList) - Method in class etomica.potential.P4BondTorsion
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P4BondTorsion
-
- gradient - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- gradient(IAtomList) - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P4BondTorsionOPLS
-
- gradient - Variable in class etomica.potential.P4TorsionDreiding
-
- gradient(IAtomList, Tensor) - Method in class etomica.potential.P4TorsionDreiding
-
- gradient(IAtomList) - Method in class etomica.potential.P4TorsionDreiding
-
- gradient - Variable in class etomica.potential.Potential2SoftSpherical
-
- gradient(IAtomList) - Method in class etomica.potential.Potential2SoftSpherical
-
Gradient of the pair potential as given by the du(double) method.
- gradient(IAtomList, Tensor) - Method in class etomica.potential.Potential2SoftSpherical
-
- gradient - Variable in class etomica.potential.Potential2SoftSphericalLS
-
- gradient(IAtomList) - Method in class etomica.potential.Potential2SoftSphericalLS
-
Gradient of the pair potential as given by the du(double) method.
- gradient(IAtomList, Tensor) - Method in class etomica.potential.Potential2SoftSphericalLS
-
- gradient(IMoleculeList) - Method in class etomica.potential.PotentialGroupSoft
-
- gradient(IMoleculeList, Tensor) - Method in class etomica.potential.PotentialGroupSoft
-
- gradient(IMoleculeList) - Method in interface etomica.potential.PotentialMolecularSoft
-
Returns the gradient of the potential as it applies to each atom in the
given AtomSet, indicating how the energy would change as the position of
the first atom is varied.
- gradient(IMoleculeList, Tensor) - Method in interface etomica.potential.PotentialMolecularSoft
-
Returns the same gradient as gradient(IMoleculeList) and also adds in
the contribution of the molecules to the pressureTensor.
- gradient(IAtomList) - Method in interface etomica.potential.PotentialSoft
-
Returns the gradient of the potential as it applies to each atom in the
given AtomSet, indicating how the energy would change as the position of
the first atom is varied.
- gradient(IAtomList, Tensor) - Method in interface etomica.potential.PotentialSoft
-
Returns the same gradient as gradient(AtomSet) and also adds in the
contribution of the AtomSet to the pressureTensor.
- gradient(IMoleculeList, Tensor) - Method in class etomica.rotation.P2LJDipole
-
- gradient(IMoleculeList) - Method in class etomica.rotation.P2LJDipole
-
- gradient2 - Variable in class etomica.potential.EwaldSummation.P2EwaldReal
-
- gradientAndTorque - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- gradientAndTorque(IAtomList) - Method in class etomica.models.co2.P2CO2H2OWheatley
-
- gradientAndTorque - Variable in class etomica.models.co2.P2CO2Hellmann
-
- gradientAndTorque(IAtomList) - Method in class etomica.models.co2.P2CO2Hellmann
-
- gradientAndTorque - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- gradientAndTorque(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- gradientAndTorque - Variable in class etomica.models.water.P2Water3PSoft
-
- gradientAndTorque(IMoleculeList) - Method in class etomica.models.water.P2Water3PSoft
-
- gradientAndTorque - Variable in class etomica.models.water.P2Water4PSoft
-
- gradientAndTorque(IMoleculeList) - Method in class etomica.models.water.P2Water4PSoft
-
- gradientAndTorque(IAtomList) - Method in class etomica.models.water.P2WaterSzalewicz
-
- gradientAndTorque(IMoleculeList) - Method in interface etomica.potential.IPotentialMolecularTorque
-
- gradientAndTorque(IAtomList) - Method in interface etomica.potential.IPotentialTorque
-
- gradientAndTorque - Variable in class etomica.potential.P2HSDipole
-
- gradientAndTorque(IMoleculeList) - Method in class etomica.potential.P2HSDipole
-
- gradientAndTorque - Variable in class etomica.potential.P2LJDipole
-
- gradientAndTorque(IMoleculeList) - Method in class etomica.potential.P2LJDipole
-
- gradientAndTorque - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- gradientAndTorque(IMoleculeList) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- gradientAndTorque - Variable in class etomica.potential.P2NitrogenHellmann
-
- gradientAndTorque(IAtomList) - Method in class etomica.potential.P2NitrogenHellmann
-
- gradientAndTorque - Variable in class etomica.potential.P2ReactionFieldDipole
-
- gradientAndTorque(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole
-
- gradientAndTorque - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- gradientAndTorque(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- gradientAndTorque - Variable in class etomica.rotation.P2LJDipole
-
- gradientAndTorque(IMoleculeList) - Method in class etomica.rotation.P2LJDipole
-
- gradients - Variable in class etomica.potential.PotentialGroupSoft
-
- GraftAction(int) - Constructor for class etomica.modules.colloid.ColloidGraphic.GraftAction
-
- graftVectors - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- GrainBoundaryConfiguration - Class in etomica.config
-
- GrainBoundaryConfiguration(BravaisLatticeCrystal, BravaisLatticeCrystal, Space) - Constructor for class etomica.config.GrainBoundaryConfiguration
-
Construct class that will place atoms on sites of the given lattices,
proceeding in the order resulting from iteration through the given index
iterator.
- GrainBoundaryTiltConfiguration - Class in etomica.config
-
- GrainBoundaryTiltConfiguration(BravaisLatticeCrystal, BravaisLatticeCrystal, ISpecies[], double, Space) - Constructor for class etomica.config.GrainBoundaryTiltConfiguration
-
- Gram - Class in etomica.units
-
- Graph - Interface in etomica.graph.model
-
- GraphExtract - Class in etomica.graph.operations
-
This class takes the given nodes from the given graph and returns a new
graph consisting only of those nodes (and the bonds between them).
- GraphExtract() - Constructor for class etomica.graph.operations.GraphExtract
-
- GraphFactory - Class in etomica.graph.model
-
- GraphFactory() - Constructor for class etomica.graph.model.GraphFactory
-
- graphHasEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheim2Site
-
- graphHasEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheim2SiteRho
-
- graphHasEdgeColor(Graph, char) - Static method in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho
-
- graphHasEdgeColor(Graph, char) - Static method in class etomica.virial.cluster.VirialDiagrams
-
- graphHasEdgeColor(Graph, char) - Static method in class etomica.virial.cluster.VirialDiagramsMix2
-
- graphHasEdgeColor(Graph, char) - Static method in class etomica.virial.cluster.VirialDiagramsPT
-
- graphic() - Method in class etomica.graphics.DefaultToolbar
-
- graphic(Object) - Method in class etomica.graphics.Device
-
- graphic() - Method in class etomica.graphics.Device
-
Same as graphic method with a null argument.
- graphic(Object) - Method in class etomica.graphics.DeviceBox
-
- graphic(Object) - Method in class etomica.graphics.DeviceButton
-
Returns the GUI element for display in the simulation.
- graphic(Object) - Method in class etomica.graphics.DeviceButtonGroup
-
- graphic(Object) - Method in class etomica.graphics.DeviceCheckBox
-
Returns the GUI box element for display in the simulation.
- graphic() - Method in class etomica.graphics.DeviceDelaySlider
-
- graphic() - Method in class etomica.graphics.DevicePlotPoints
-
Returns the top level panel that the function plot components sit on.
- graphic(Object) - Method in class etomica.graphics.DeviceSelector
-
Returns the GUI element for display in the simulation.
- graphic(Object) - Method in class etomica.graphics.DeviceSlider
-
Returns the GUI element for display in the simulation.
- graphic(Object) - Method in class etomica.graphics.DeviceSpinner
-
Returns the GUI element for display in the simulation.
- graphic(Object) - Method in class etomica.graphics.DeviceTable
-
Returns the top level panel that the table components sit on.
- graphic(Object) - Method in class etomica.graphics.DeviceThermoSelector
-
Returns the GUI element for display in the simulation.
- graphic(Object) - Method in class etomica.graphics.DeviceThermoSlider
-
- graphic(Object) - Method in class etomica.graphics.DeviceToggleRadioButtons
-
Returns the GUI button element for display in the simulation.
- graphic(Object) - Method in class etomica.graphics.DeviceTrioControllerButton
-
Returns the JPanel that contains the buttons.
- graphic(Object) - Method in class etomica.graphics.Display
-
Method of Simulation.GraphicElement interface.
- graphic() - Method in class etomica.graphics.Display
-
Same as graphic method with a null argument.
- graphic(Object) - Method in class etomica.graphics.DisplayBox
-
Simulation.GraphicalElement interface method.
- graphic(Object) - Method in class etomica.graphics.DisplayPlot
-
Overrides superclass method to return a JPanel holding the plot.
- graphic(Object) - Method in class etomica.graphics.DisplayPolytope
-
Simulation.GraphicalElement interface method.
- graphic(Object) - Method in class etomica.graphics.DisplayTable
-
- graphic(Object) - Method in class etomica.graphics.DisplayTextBox
-
- graphic(Object) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- graphic(Object) - Method in interface etomica.graphics.GraphicalElement
-
Interface for a Simulation element that would be used in a simulation graphical user interface (GUI)
- graphic - Variable in class etomica.modules.droplet.EllipseDisplayAction
-
- graphic() - Method in class etomica.modules.osmosis.Osmosis.InitializeMolecules
-
- graphic(Object) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- graphic(Object) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
- graphic(Object) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- graphic(Object) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
- graphic(Object) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
- graphic(Object) - Method in class etomica.zeolite.DeviceButtonSingle
-
Returns the GUI element for display in the simulation.
- GRAPHIC_ONLY - Static variable in class etomica.graphics.SimulationGraphic
-
- GraphicalElement - Interface in etomica.graphics
-
Interface for a simulation element that can make a graphical component
- graphicOut - Variable in class etomica.modules.clustergenerator.MyApplet
-
- graphicOut2 - Variable in class etomica.modules.clustergenerator.MyApplet
-
- graphics - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- graphics - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
-
- graphics - Variable in class etomica.freeenergy.npath.SimLattice.LjMC3DParams
-
- graphics - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
-
- graphics - Variable in class etomica.interfacial.LJMC.LjMC3DParams
-
- graphics - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- graphics - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
-
- graphics - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- graphics - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- graphics - Variable in class etomica.mappedvirial.MappedU.LJMDParams
-
- graphics - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
-
- graphics - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
-
- graphics - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
-
- graphics - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- graphics - Static variable in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol
-
- graphics - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- graphics - Static variable in class etomica.virial.simulations.VirialTraPPEAlcohol
-
- Graphics3D - Class in org.jmol.g3d
-
Provides high-level graphics primitives for 3D visualization
for the software renderers.
- Graphics3D() - Constructor for class org.jmol.g3d.Graphics3D
-
- graphicsForMetrics - Variable in class org.jmol.util.GData
-
- graphicsPanel - Variable in class etomica.graphics.SimulationPanel
-
- graphicsToggler - Variable in class etomica.modules.clustergenerator.MyApplet
-
- GraphicsToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.GraphicsToggler
-
- GraphImpl - Class in etomica.graph.model.impl
-
- GraphImpl(Node[]) - Constructor for class etomica.graph.model.impl.GraphImpl
-
- GraphImpl(byte) - Constructor for class etomica.graph.model.impl.GraphImpl
-
- GraphImpl(byte, byte) - Constructor for class etomica.graph.model.impl.GraphImpl
-
- GraphImpl(byte, Bitmap) - Constructor for class etomica.graph.model.impl.GraphImpl
-
- GraphImpl(byte, byte, Bitmap) - Constructor for class etomica.graph.model.impl.GraphImpl
-
- GraphImpl(byte, byte, Bitmap, Coefficient) - Constructor for class etomica.graph.model.impl.GraphImpl
-
- GraphIterator - Interface in etomica.graph.model
-
- GraphList<E> - Class in etomica.graph.model
-
- GraphList() - Constructor for class etomica.graph.model.GraphList
-
- GraphList(Comparator<E>) - Constructor for class etomica.graph.model.GraphList
-
- GraphMap - Class in etomica.graph.viewer
-
- GraphMap(Set<Graph>, JComponent) - Constructor for class etomica.graph.viewer.GraphMap
-
- GraphNumber - Class in etomica.graph.util
-
- GraphNumber() - Constructor for class etomica.graph.util.GraphNumber
-
- GraphOp - Interface in etomica.graph.operations
-
Interface for a simple operation that takes a Graph and returns a Graph.
- graphOp - Variable in class etomica.graph.operations.MaxIsomorph.MaxIsomorphParameters
-
- GraphOp.GraphOpNull - Class in etomica.graph.operations
-
A dummy implementation of GraphOp that does nothing.
- GraphOpMaxRoot - Class in etomica.graph.operations
-
GraphOp class that adjusts root points in each component so that
+ the number of root points is maintained
+ no component has more than one root point
+ all root points are included in all the "earliest" components
+ if a component has a root point, it is the first node in that component
This class only makes sense if the specific identity of each root
point is unimportant (Metadata.ROOT_POINTS_SPECIAL=false).
- GraphOpMaxRoot() - Constructor for class etomica.graph.operations.GraphOpMaxRoot
-
- GraphOpNull() - Constructor for class etomica.graph.operations.GraphOp.GraphOpNull
-
- graphs - Static variable in class etomica.graph.isomorphism.Match
-
- graphSegment - Variable in class etomica.graph.property.FFTDecomposition
-
- graphSplitter - Variable in class etomica.graph.operations.Unfactor
-
- GRAY - Static variable in class org.jmol.util.Colix
-
- GREATER_THAN - Static variable in class etomica.compatibility.Feature
-
- GREEN - Static variable in class org.jmol.util.Colix
-
- greenLight - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- greenLight - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- greys - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- greyscalerendering - Static variable in class org.jmol.script.Token
-
- group - Static variable in class org.jmol.script.Token
-
- group1 - Static variable in class org.jmol.script.Token
-
- groupid - Static variable in class org.jmol.script.Token
-
- GROUPID_AMINO_MAX - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_ARGININE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_ASPARAGINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_ASPARTATE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_CYSTEINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_GLUTAMATE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_GLUTAMINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_HISTIDINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_LYSINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_NUCLEIC_MAX - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_PROLINE - Static variable in class org.jmol.viewer.JmolConstants
-
- GROUPID_TRYPTOPHAN - Static variable in class org.jmol.viewer.JmolConstants
-
- groupindex - Static variable in class org.jmol.script.Token
-
- groupScaler - Variable in class etomica.action.BoxInflate
-
- groupStart - Static variable in class etomica.virial.cluster.VirialDiagrams
-
- groupTag - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- groupTranslationVector - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- groupTranslationVector - Variable in class etomica.association.BiasVolumeAceticAcid
-
- groupTranslationVector - Variable in class etomica.association.MCMoveBiasUBMolecule
-
- groupTranslationVector - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- groupTranslationVector - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- groupTransVect - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- groupTransVect - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- groupTransVect - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- groupTransVect - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- growMolecule - Variable in class etomica.models.hexane.TestHexane
-
- growMolecule - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
-
- growMolecule - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- growMolecule - Variable in class etomica.models.hexane.TestSetToUHexane
-
- growto(BigInteger) - Method in class etomica.veos.bigdecimal.Prime
-
extend the list of known primes up to n
- gruneisen_knu - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- gSat - Variable in class etomica.interfacial.P1Wall
-
- gScaled - Variable in class org.jmol.util.Rgb16
-
- gSet1 - Variable in class etomica.graph.operations.UnaryChain
-
- GSTAR - Variable in class etomica.math.Gamma
-
- gSum - Variable in class etomica.data.meter.MeterDihedralAngle
-
- gSum - Variable in class etomica.data.meter.MeterRDF
-
- gSum - Variable in class etomica.data.meter.PotentialCalculationRDF
-
- gSum - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- gtmp - Variable in class etomica.potential.P4BondTorsion
-
- gtmp - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- GUI - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam
-
- i(double, int) - Method in class etomica.modules.droplet.IntegratorDroplet
-
- I - Variable in class etomica.potential.P3Induction
-
- I - Variable in class etomica.potential.PotentialCalculationPressureTensor
-
- i2roots() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Generate the factors which are 2nd degree polynomials.
- iA - Variable in class org.jmol.util.MeshSurface
-
- IAction - Interface in etomica.action
-
General interface for performing an action, allowing the defined behavior to be separated from the driver that causes
it.
- IAPIPotential - Interface in etomica.normalmode
-
Preliminary interface for proposed IPotential interface
- iasdone - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- IAssociationHelper - Interface in etomica.association
-
Interface for a class that is capable of populating a list of atoms in an
smer as well as checking the validity of the bonding
- IAssociationHelperMolecule - Interface in etomica.association
-
Interface for a class that is capable of populating a list of molecules in an
smer as well as checking the validity of the bonding
- IAtom - Interface in etomica.atom
-
IAtom is an interface for atoms in the simulation.
- IAtomKinetic - Interface in etomica.atom
-
Interface for an atom that holds vectors for velocity.
- IAtomList - Interface in etomica.atom
-
Interface for a list of IAtoms.
- IAtomOriented - Interface in etomica.atom
-
Interface for a IAtom that includes an IVector that defines the atom's
orientation.
- IAtomOrientedKinetic - Interface in etomica.atom
-
Interface for an Atom that has a position, orientation, velocity and angular
velocity.
- iB - Variable in class org.jmol.util.MeshSurface
-
- IBigValue - Interface in etomica.veos
-
- iC - Variable in class org.jmol.util.MeshSurface
-
- icc - Variable in class etomica.potential.P2WaterPotentialsJankowski
-
- ICollectionPotential - Interface in etomica.virial.GUI.components
-
- IConformation - Interface in etomica.config
-
- IConformationOriented - Interface in etomica.config
-
- iCorner - Variable in class etomica.util.Grabber.ActionCornerSetter
-
- iCorner - Variable in class etomica.util.Grabber.CornerSetListener
-
- id - Variable in class etomica.action.ActionMinimizeEnergy
-
- id - Variable in class etomica.freeenergy.npath.DataSourceEnergies
-
- id - Variable in class etomica.interfacial.MeterWallForce
-
- id - Variable in class etomica.normalmode.MeterDADB
-
- id - Variable in class etomica.normalmode.MeterSolidProps
-
- id - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- id - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- id - Variable in class etomica.server.representations.PropertyUpdate
-
- id - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- id - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- ID - Variable in class etomica.virial.CoordinatePairLeafSet
-
- ID - Variable in class etomica.virial.CoordinatePairMoleculeSet
-
- id - Variable in enum org.jmol.constant.EnumPalette
-
- IData - Interface in etomica.data
-
Abstract container of simulation data and information describing it.
- IDataInfo - Interface in etomica.data
-
- IDataInfoFactory - Interface in etomica.data
-
- IDataSink - Interface in etomica.data
-
A recipient of Data.
- IDataSource - Interface in etomica.data
-
Interface for an object that can provide IData objects
on request.
- IDEAL_GAS - Static variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- IdenticalFree - Class in etomica.graph.operations
-
Operation that removes identical graphs
- IdenticalFree() - Constructor for class etomica.graph.operations.IdenticalFree
-
- IdenticalGraphFilter - Class in etomica.graph.iterators.filters
-
Filter that combines graphs that are identical
- IdenticalGraphFilter(GraphIterator) - Constructor for class etomica.graph.iterators.filters.IdenticalGraphFilter
-
- identifier - Static variable in class org.jmol.script.Token
-
- identify - Static variable in class org.jmol.script.Token
-
- Identity() - Constructor for class etomica.math.function.Function.Identity
-
- identity - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- identity - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- identity - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- identity - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- identity - Variable in class etomica.modules.droplet.IntegratorDroplet
-
- identity - Variable in class etomica.potential.EwaldSummation
-
- identity - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- idFontFace - Variable in class org.jmol.util.JmolFont
-
- idFontStyle - Variable in class org.jmol.util.JmolFont
-
- idFreeEnergy(double) - Method in class etomica.statmech.HardSphere
-
Returns the ideal gas free energy for the given density.
- idFreeEnergy(double) - Static method in class etomica.statmech.HardSphereSolid
-
Returns the ideal gas free energy for the given density.
- iDiagram - Variable in class etomica.virial.ClusterSumStickyEF
-
- iDipole - Variable in class etomica.potential.P2ReactionFieldDipole
-
- iDipole - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- idonl - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- ids - Variable in class etomica.virial.PotentialEmulCached
-
- idx - Variable in class etomica.lattice.crystal.Primitive
-
- idx - Variable in class etomica.modules.statistics.DataAccPusher
-
- IEGenerator - Class in etomica.virial
-
- IEGenerator() - Constructor for class etomica.virial.IEGenerator
-
- IElement - Interface in etomica.chem.elements
-
- iEmbed - Variable in class etomica.potential.P2WaterPotentialsJankowski
-
- IEvent - Interface in etomica.util
-
- ifactor() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Factorization into integer polynomials.
- Ifactor - Class in etomica.veos.bigdecimal
-
Factored integers.
- Ifactor(int) - Constructor for class etomica.veos.bigdecimal.Ifactor
-
Constructor given an integer.
- Ifactor(BigInteger) - Constructor for class etomica.veos.bigdecimal.Ifactor
-
Constructor given a BigInteger .
- Ifactor(Vector<Integer>) - Constructor for class etomica.veos.bigdecimal.Ifactor
-
Constructor given a list of exponents of the prime factor decomposition.
- Ifactor(Ifactor) - Constructor for class etomica.veos.bigdecimal.Ifactor
-
Copy constructor.
- IFLGST - Variable in class etomica.math.Gamma
-
- IFunction - Interface in etomica.math.function
-
- ig - Variable in class etomica.modules.mu.MeterDensitySides
-
- ignoredAtomType - Variable in class etomica.modules.chainequilibrium.MeterChainLength
-
- ignoreOverlap - Variable in class etomica.action.SimulationRestart
-
- ignoreOverlap - Variable in class etomica.modules.mu.P2SquareWellOneSide
-
- ignoreOverlap - Variable in class etomica.potential.P2HardSphere
-
- ignoreOverlap - Variable in class etomica.potential.P2PenetrableSquareWell
-
- ignoreOverlap - Variable in class etomica.potential.P2SquareWell
-
- ignoreOverlap - Variable in class etomica.potential.P2SquareWellRobust
-
- IgnoreProperty - Annotation Type in etomica.meta.annotations
-
When applied to a get method, this annotation marks the property as ignored when introspecting the
simulation.
- iGraph - Variable in class etomica.virial.simulations.VirialLJBridge.VirialLJParam
-
- ijInit(double[], double[][], Unit) - Method in class etomica.models.co2.P2CO2Hellmann
-
- ijk - Variable in class etomica.models.water.P2WaterSzalewicz
-
- ijRTensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- ijRTensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- ijRTensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- ijRTensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- ijTensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- ijTensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- ijTensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- ijTensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- IListener<E extends IEvent> - Interface in etomica.util
-
- imageOrigins(int) - Method in class etomica.space.Boundary
-
Set of vectors describing the displacements needed to translate the
central image to all of the periodic images.
- imageOrigins(int) - Method in class etomica.space.BoundaryDeformablePeriodic
-
- imageOrigins(int) - Method in class etomica.space.BoundaryRectangular
-
Returns a set of image origins for a set of periodic image shells.
- imageOrigins(int) - Method in class etomica.space.BoundaryRectangularNonperiodic
-
Returns a zero-length vector.
- imageOrigins(int) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
-
- imageOut(String) - Method in class etomica.graph.viewer.GraphMap
-
- ImagePanel() - Constructor for class etomica.util.Grabber.ImagePanel
-
Constructor sets default size of the plot
- ImagePanel(Color, int, int) - Constructor for class etomica.util.Grabber.ImagePanel
-
- ImageShell - Class in g3dsys.images
-
- ImageShell(G3DSys) - Constructor for class g3dsys.images.ImageShell
-
- imagestate - Static variable in class org.jmol.script.Token
-
- imaginary() - Method in class etomica.math.Complex
-
Imaginary part of this Complex number,the y-coordinate in rectangular coordinates.
- imaginaryT - Variable in class etomica.normalmode.MeterHarmonicCoordinate
-
- imaginaryT - Variable in class etomica.normalmode.MeterHarmonicEnergy
-
- imaginaryT - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- imaginaryT - Variable in class etomica.normalmode.MeterNormalMode
-
- imax - Variable in class etomica.conjugategradient.ConjugateGradients
-
- imax - Variable in class etomica.conjugategradient.NonLinearConjugateGradients
-
- imax - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- imax - Variable in class etomica.conjugategradient.SteepestDescent
-
- imgPanel - Variable in class etomica.util.Grabber
-
- IMolecularModel_SpeciesFactory - Interface in etomica.virial.GUI.models
-
- IMolecule - Interface in etomica.molecule
-
Interface for an IMolecule
- iMolecule - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- iMolecule - Variable in class etomica.virial.MCMoveClusterRingScale
-
- IMoleculeKinetic - Interface in etomica.molecule
-
Interface for an molecule that holds vectors for velocity.
- IMoleculeList - Interface in etomica.molecule
-
Interface for a set of IAtoms.
- IMoleculeOriented - Interface in etomica.molecule
-
Interface for a IAtom that includes an IVector that defines the atom's
position.
- IMoleculeOrientedKinetic - Interface in etomica.molecule
-
Interface for an Atom that has a position, orientation, velocity and angular
velocity.
- IMoleculePositionDefinition - Interface in etomica.molecule
-
Returns a vector given a molecule, thereby defining the position
of the molecule.
- IMoleculePositioned - Interface in etomica.molecule
-
- iMon - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- iMonomer - Variable in class etomica.potential.P2WaterPotentialsJankowski
-
- inc() - Method in interface etomica.graph.model.Bitmap
-
Increments the integer value of this bitmap by one: bitmap++.
- inc() - Method in class etomica.graph.model.impl.AbstractBitmap
-
- includeAntibiasErr - Variable in class etomica.overlap.DataOverlap
-
- includeLrc - Variable in class etomica.potential.IteratorDirective
-
Flag indicating whether long-range correction contributions should
be included in calculation.
- includeM - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- includeM - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- INCOMPATIBLE_TYPES - Static variable in class etomica.compatibility.Feature
-
- increment(int[]) - Method in class etomica.lattice.RectangularLattice
-
- increment(int) - Method in class org.jmol.script.ScriptVariable
-
- ind3_beta - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind3_gamma - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind3_R0 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind_beta - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind_C10 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind_C6 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind_C8 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind_charge - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind_d1 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind_d10 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind_d6 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind_d8 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- ind_lin - Variable in class etomica.models.water.P2WaterSzalewicz
-
- inDataInfo - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
-
- index - Variable in class etomica.atom.Atom
-
- index - Variable in class etomica.atom.AtomType
-
- index - Variable in class etomica.atom.iterator.ApiIndexList
-
- index - Variable in class etomica.box.BoxAtomIndexEvent
-
- index - Variable in class etomica.box.BoxIndexEvent
-
- index - Variable in class etomica.box.BoxMoleculeIndexEvent
-
- index - Variable in class etomica.data.AccumulatorAverage.StatType
-
- index - Variable in class etomica.data.AccumulatorAverageBlockless.StatType
-
- index - Variable in class etomica.data.AccumulatorAverageBlocklessSlim.StatType
-
- index - Variable in class etomica.data.DataSet.DataSetSink
-
- index - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- index - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- index - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- index - Variable in class etomica.molecule.Molecule
-
- index - Variable in class etomica.species.Species
-
- index - Variable in class org.jmol.script.ScriptVariable
-
- index - Variable in class org.jmol.util.Point3fi
-
- indexaC - Static variable in class etomica.models.rowley.SpeciesEthanol
-
- indexaC - Static variable in class etomica.models.rowley.SpeciesMethanol
-
- indexaH - Static variable in class etomica.models.rowley.SpeciesEthanol
-
- indexaH - Static variable in class etomica.models.rowley.SpeciesMethanol
-
- indexAtom1 - Static variable in class etomica.normalmode.SpeciesHSDimer
-
- indexAtom2 - Static variable in class etomica.normalmode.SpeciesHSDimer
-
- indexC - Static variable in class etomica.AlkaneEH.SpeciesMethane
-
- indexC - Static variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- indexC - Static variable in class etomica.models.rowley.SpeciesEthanol
-
- indexC - Static variable in class etomica.models.water.SpeciesWater4PCOM
-
- indexC - Static variable in class etomica.paracetamol.SpeciesParacetamol
-
- indexC - Static variable in class etomica.virial.SpeciesMethane
-
- indexC - Static variable in class etomica.virial.SpeciesTraPPECO2
-
- indexC1 - Static variable in class etomica.virial.SpeciesAnthracene3site464
-
- indexC1 - Static variable in class etomica.virial.SpeciesAnthracene3site545
-
- indexC1 - Static variable in class etomica.virial.SpeciesPh3site464
-
- indexC1 - Static variable in class etomica.virial.SpeciesPh3site545
-
- indexC1 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexC1 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- indexC1 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexC2 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexC2 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- indexC2 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexC3 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexC3 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexC4 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexC4 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexC_3_1 - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- indexC_3_2 - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- indexCenter - Static variable in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- indexCH1 - Static variable in class etomica.virial.SpeciesAnthracene3site464
-
- indexCH1 - Static variable in class etomica.virial.SpeciesAnthracene3site545
-
- indexCH1 - Static variable in class etomica.virial.SpeciesPh3site464
-
- indexCH1 - Static variable in class etomica.virial.SpeciesPh3site545
-
- indexCH1 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexCH1 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- indexCH1 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexCH10 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexCH10 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexCH2 - Static variable in class etomica.virial.SpeciesAnthracene3site464
-
- indexCH2 - Static variable in class etomica.virial.SpeciesAnthracene3site545
-
- indexCH2 - Static variable in class etomica.virial.SpeciesPh3site464
-
- indexCH2 - Static variable in class etomica.virial.SpeciesPh3site545
-
- indexCH2 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexCH2 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- indexCH2 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexCH3 - Static variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- indexCH3 - Static variable in class etomica.models.traPPE.SpeciesMethanol
-
- indexCH3 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexCH3 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- indexCH3 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexCH4 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexCH4 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- indexCH4 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexCH5 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexCH5 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- indexCH5 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexCH6 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexCH6 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- indexCH6 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexCH7 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexCH7 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- indexCH7 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexCH8 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexCH8 - Static variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- indexCH8 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexCH9 - Static variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- indexCH9 - Static variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- indexDBO - Static variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- indexed - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Should output Image be indexed .
- indexer - Variable in class etomica.data.DataDistributer
-
- indexF1 - Static variable in class etomica.virial.Species7SiteRigidSF6
-
- indexF2 - Static variable in class etomica.virial.Species7SiteRigidSF6
-
- indexF3 - Static variable in class etomica.virial.Species7SiteRigidSF6
-
- indexF4 - Static variable in class etomica.virial.Species7SiteRigidSF6
-
- indexF5 - Static variable in class etomica.virial.Species7SiteRigidSF6
-
- indexF6 - Static variable in class etomica.virial.Species7SiteRigidSF6
-
- indexH - Static variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- indexH - Static variable in class etomica.models.traPPE.SpeciesMethanol
-
- indexH - Static variable in class etomica.paracetamol.SpeciesParacetamol
-
- indexH1 - Static variable in class etomica.AlkaneEH.SpeciesMethane
-
- indexH1 - Static variable in class etomica.models.rowley.SpeciesMethanol
-
- indexH1 - Static variable in class etomica.models.water.SpeciesWater3P
-
- indexH1 - Static variable in class etomica.models.water.SpeciesWater3POriented
-
- indexH1 - Static variable in class etomica.models.water.SpeciesWater4P
-
- indexH1 - Static variable in class etomica.models.water.SpeciesWater4PCOM
-
- indexH1 - Static variable in class etomica.models.water.SpeciesWater4POriented
-
- indexH1 - Static variable in class etomica.virial.SpeciesMethane
-
- indexH1a - Static variable in class etomica.models.rowley.SpeciesEthanol
-
- indexH1b - Static variable in class etomica.models.rowley.SpeciesEthanol
-
- indexH2 - Static variable in class etomica.AlkaneEH.SpeciesMethane
-
- indexH2 - Static variable in class etomica.models.water.SpeciesWater3P
-
- indexH2 - Static variable in class etomica.models.water.SpeciesWater3POriented
-
- indexH2 - Static variable in class etomica.models.water.SpeciesWater4P
-
- indexH2 - Static variable in class etomica.models.water.SpeciesWater4PCOM
-
- indexH2 - Static variable in class etomica.models.water.SpeciesWater4POriented
-
- indexH2 - Static variable in class etomica.virial.SpeciesMethane
-
- indexH2a - Static variable in class etomica.models.rowley.SpeciesEthanol
-
- indexH2a - Static variable in class etomica.models.rowley.SpeciesMethanol
-
- indexH2b - Static variable in class etomica.models.rowley.SpeciesEthanol
-
- indexH2b - Static variable in class etomica.models.rowley.SpeciesMethanol
-
- indexH2c - Static variable in class etomica.models.rowley.SpeciesEthanol
-
- indexH3 - Static variable in class etomica.AlkaneEH.SpeciesMethane
-
- indexH3 - Static variable in class etomica.virial.SpeciesMethane
-
- indexH4 - Static variable in class etomica.AlkaneEH.SpeciesMethane
-
- indexH4 - Static variable in class etomica.virial.SpeciesMethane
-
- indexHp - Static variable in class etomica.paracetamol.SpeciesParacetamol
-
- indexIterator - Variable in class etomica.config.ConfigurationLattice
-
- indexIterator - Variable in class etomica.config.ConfigurationLatticeSimple
-
- IndexIterator - Interface in etomica.lattice
-
Loops through the set of indexes appropriate to a lattice of given size.
- indexIterator - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
- indexIterator - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
- IndexIterator - Interface in g3dsys.control
-
- IndexIteratorIncreasing - Class in etomica.lattice
-
Iterator that returns indices in increasing order, starting at 0 and ending
including all indices where |i| <= max, where i are the components of the
index.
- IndexIteratorIncreasing(int) - Constructor for class etomica.lattice.IndexIteratorIncreasing
-
- IndexIteratorRectangular - Class in etomica.lattice
-
Iterates arrays of int, such that 0 <= a[0] <= size[0], 0 <= a[1] <= size[1], etc.,
thereby spanning a rectangular region.
- IndexIteratorRectangular(int) - Constructor for class etomica.lattice.IndexIteratorRectangular
-
Constructs iterator that returns int arrays of length D.
- IndexIteratorReflecting - Class in etomica.lattice
-
Generates iterates by alternately keeping or flipping the sign of each element of
iterates generated by another iterator.
- IndexIteratorReflecting(IndexIterator) - Constructor for class etomica.lattice.IndexIteratorReflecting
-
Constructs iterator to generate reflections from iterates of
given iterator.
- IndexIteratorSizable - Interface in etomica.lattice
-
Interface for an iterator in which the number of indices
in each dimension may be specified.
- IndexIteratorTriangular - Class in etomica.lattice
-
Iterates arrays of int such that a[0] >= a[1] >= ...
- IndexIteratorTriangular(int) - Constructor for class etomica.lattice.IndexIteratorTriangular
-
Constructs iterator that will return int arrays of length D.
- IndexIteratorTriangularPermutations - Class in etomica.lattice
-
Generates all unique iterates formed as permutations of iterates given by IndexIteratorTriangular with
allowEqualElements set to true.
- IndexIteratorTriangularPermutations(int) - Constructor for class etomica.lattice.IndexIteratorTriangularPermutations
-
- indexM - Static variable in class etomica.models.water.SpeciesWater4P
-
- indexM - Static variable in class etomica.models.water.SpeciesWater4PCOM
-
- indexM - Static variable in class etomica.models.water.SpeciesWater4POriented
-
- IndexMap<V> - Class in etomica.util.collections
-
An specialized implementation of Map which is designed for mapping
an index to a value.
- IndexMap() - Constructor for class etomica.util.collections.IndexMap
-
Creates a new map with the default initial capacity of 10 and
default reservoir size of 30.
- IndexMap(int) - Constructor for class etomica.util.collections.IndexMap
-
Creates a new map with the given initial capacity and default
reservoir size of 30.
- IndexMap(int, int) - Constructor for class etomica.util.collections.IndexMap
-
Creates a new map with the given initial capacity and reservoir size.
- indexN - Static variable in class etomica.paracetamol.SpeciesParacetamol
-
- indexN1 - Static variable in class etomica.models.nitrogen.SpeciesN2
-
- indexN1 - Static variable in class etomica.models.nitrogen.SpeciesN2B
-
- indexN1 - Static variable in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- indexN2 - Static variable in class etomica.models.nitrogen.SpeciesN2
-
- indexN2 - Static variable in class etomica.models.nitrogen.SpeciesN2B
-
- indexN2 - Static variable in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- indexO - Static variable in class etomica.models.rowley.SpeciesEthanol
-
- indexO - Static variable in class etomica.models.rowley.SpeciesMethanol
-
- indexO - Static variable in class etomica.models.traPPE.SpeciesMethanol
-
- indexO - Static variable in class etomica.models.water.SpeciesWater3P
-
- indexO - Static variable in class etomica.models.water.SpeciesWater3POriented
-
- indexO - Static variable in class etomica.models.water.SpeciesWater4P
-
- indexO - Static variable in class etomica.models.water.SpeciesWater4PCOM
-
- indexO - Static variable in class etomica.models.water.SpeciesWater4POriented
-
- indexO - Static variable in class etomica.paracetamol.SpeciesParacetamol
-
- indexOf(IAtom) - Method in class etomica.atom.AtomArrayList
-
- indexOf(IMolecule) - Method in class etomica.molecule.MoleculeArrayList
-
- indexOf(IAtom) - Method in class etomica.potential.P2HardBondedList.BondArrayList
-
- indexOf(String) - Method in class org.jmol.util.StringXBuilder
-
- indexOf2(String, int) - Method in class org.jmol.util.StringXBuilder
-
- indexOleft - Static variable in class etomica.virial.SpeciesTraPPECO2
-
- indexOright - Static variable in class etomica.virial.SpeciesTraPPECO2
-
- indexP1left - Static variable in class etomica.models.nitrogen.SpeciesN2
-
- indexP1left - Static variable in class etomica.models.nitrogen.SpeciesN2B
-
- indexP1left - Static variable in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- indexP1right - Static variable in class etomica.models.nitrogen.SpeciesN2
-
- indexP1right - Static variable in class etomica.models.nitrogen.SpeciesN2B
-
- indexP1right - Static variable in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- indexP2left - Static variable in class etomica.models.nitrogen.SpeciesN2
-
- indexP2left - Static variable in class etomica.models.nitrogen.SpeciesN2B
-
- indexP2right - Static variable in class etomica.models.nitrogen.SpeciesN2
-
- indexP2right - Static variable in class etomica.models.nitrogen.SpeciesN2B
-
- indexS - Static variable in class etomica.virial.Species7SiteRigidSF6
-
- indexSBO - Static variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- indexSelectedSpecies - Variable in exception etomica.virial.GUI.components.ExceptionDoNotRemoveSpecies
-
- indexX - Static variable in class etomica.models.rowley.SpeciesEthanol
-
- indexX - Static variable in class etomica.models.rowley.SpeciesMethanol
-
- indices - Variable in class etomica.virial.cluster.PermutationIterator
-
- indN_iter() - Method in class etomica.models.water.P2WaterSzalewicz
-
Compute the iterative induction between N water molecules
using several polarization centers in the molecular plane
- INeighborListListener - Interface in etomica.nbr.list
-
- INeighborListListenerMolecular - Interface in etomica.nbr.list.molecule
-
- inflate - Variable in class etomica.integrator.IntegratorGear4NPH
-
- inflate - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
-
- inflate - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- inflate - Variable in class etomica.models.nitrogen.MCMoveVolumeN2
-
- inflate - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
-
- inflate - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- inflate - Variable in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- inflate - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- inflate - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- inflate - Variable in class etomica.normalmode.MCMoveVolumeSolid
-
- inflate - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- inflate(Boundary) - Method in class etomica.space.BoundaryEventManager
-
- inflateEvent - Variable in class etomica.space.Boundary
-
- info - Static variable in class org.jmol.script.Token
-
- info(String) - Method in class org.jmol.util.DefaultLogger
-
- info(String) - Static method in class org.jmol.util.Logger
-
og* Writes a log at INFO level.
- info(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at INFO level.
- info2 - Variable in class etomica.meam.EFSTungsten
-
- info2 - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- info2 - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- info2 - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- info2 - Variable in class etomica.meam.MEAM_MC
-
- info2 - Variable in class etomica.meam.MEAMMd3D
-
- info2 - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- inGreyscaleMode - Variable in class org.jmol.util.GData
-
- INHERIT_ALL - Static variable in class org.jmol.util.Colix
-
- INHERIT_COLOR - Static variable in class org.jmol.util.Colix
-
- init() - Method in class etomica.graph.viewer.GraphMap
-
- init() - Method in class etomica.graphics.DeviceNSelector
-
- init() - Method in class etomica.graphics.DisplayPolytope.Applet
-
- init() - Method in class etomica.math.numerical.AkimaSplineSmootherApp.Applet
-
- init(int) - Method in class etomica.math.numerical.AkimaSplineSmootherApp
-
- init() - Method in class etomica.math.numerical.AkimaSplineSmootherDyApp.Applet
-
- init(int) - Method in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- init() - Method in class etomica.modules.adsorption.AdsorptionGraphic.Applet
-
- init() - Method in class etomica.modules.catalysis.CatalysisGraphic.Applet
-
- init() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic.Applet
-
- init() - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic.Applet
-
- init() - Method in class etomica.modules.clustergenerator.MyApplet
-
- init() - Method in class etomica.modules.colloid.ColloidGraphic.Applet
-
- init() - Method in class etomica.modules.crystalviewer.CrystalViewer.Applet
-
- init() - Method in class etomica.modules.dcvgcmd.DCVGCMDGraphic.Applet
-
- init() - Method in class etomica.modules.droplet.DropletAtomicGraphic.Applet
-
- init() - Method in class etomica.modules.droplet.DropletGraphic.Applet
-
- init() - Method in class etomica.modules.ensembles.LJMCGraphic.Applet
-
- init() - Method in class etomica.modules.entropylottery.EntropyLotteryGraphic.Applet
-
- init() - Method in class etomica.modules.insertion.InsertionGraphic.Applet
-
- init() - Method in class etomica.modules.interfacial.InterfacialSWGraphic.Applet
-
- init() - Method in class etomica.modules.joulethomson.JouleThomson.Applet
-
- init() - Method in class etomica.modules.ljmd.LjmdGraphic.Applet
-
- init() - Method in class etomica.modules.materialfracture.MaterialFractureGraphic.Applet
-
- init() - Method in class etomica.modules.mu.MuGraphic.Applet
-
- init() - Method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.Applet
-
- init() - Method in class etomica.modules.multiharmonic.MultiharmonicGraphic.Applet
-
- init() - Method in class etomica.modules.multiharmonic.MultiharmonicGraphicMC.Applet
-
- init() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.Applet
-
- init() - Method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC.Applet
-
- init() - Method in class etomica.modules.osmosis.Osmosis.Applet
-
- init() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.Applet
-
- init() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
Initialize all the bits based on previously set doConfigButton and doRDF.
- init() - Method in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.Applet
-
- init() - Method in class etomica.modules.rheology.RheologyGraphic.Applet
-
- init() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.Applet
-
- init() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.Applet
-
- init() - Method in class etomica.modules.sam.SamGraphic.Applet
-
- init() - Method in class etomica.modules.swmd.SwmdGraphic.Applet
-
- init() - Method in class etomica.modules.vle.B2Fit.Applet
-
- init() - Method in class etomica.modules.vle.VLE.Applet
-
- init() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- init() - Method in class etomica.normalmode.HTTPSoftSphereApplet.Applet
-
- init() - Method in class etomica.normalmode.MCMovePhaseAngle
-
- init() - Method in class etomica.normalmode.MCMoveWV
-
- init() - Method in class etomica.normalmode.NormalModeAnalysisDisplay1D.Applet
-
- init() - Method in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic.Applet
-
- init() - Method in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic.Applet
-
- init() - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D.Applet
-
- init() - Method in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic.Applet
-
- init() - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic.Applet
-
- init() - Method in class etomica.normalmode.SimLJVacancy.Applet
-
- init() - Method in class etomica.rotation.DipoleBox.Applet
-
- init() - Method in class etomica.rotation.DipoleBoxMatrix.Applet
-
- init() - Method in class etomica.rotation.SingleDipole.Applet
-
- init() - Method in class etomica.rotation.SingleDumbellRattle.Applet
-
- init() - Method in class etomica.rotation.SingleDumbellShake.Applet
-
- init() - Method in class etomica.rotation.SingleWater.Applet
-
- init() - Method in class etomica.rotation.SingleWaterMatrix.Applet
-
- init() - Method in class etomica.rotation.SingleWaterRattle.Applet
-
- init() - Method in class etomica.rotation.SingleWaterShake.Applet
-
- init() - Method in class etomica.rotation.WaterBox.Applet
-
- init() - Method in class etomica.rotation.WaterDroplet.Applet
-
- init() - Method in class etomica.rotation.WaterDropletMatrix.Applet
-
- init() - Method in class etomica.rotation.WaterDropletRattle.Applet
-
- init() - Method in class etomica.rotation.WaterDropletShake.Applet
-
- init() - Method in class etomica.rotation.WaterTrimer.Applet
-
- init() - Method in class etomica.rotation.WaterTrimerRattle.Applet
-
- init() - Method in class etomica.rotation.WaterTrimerShake.Applet
-
- init(EndpointConfig) - Method in class etomica.server.resources.ConfigurationWebsocket.ConfigurationUpdateEncoder
-
- init(EndpointConfig) - Method in class etomica.server.resources.data.DataStreamWebsocket.DataAndInfoEncoder
-
- init() - Method in class etomica.simulation.prototypes.LJMD3D.Applet
-
- init() - Method in class etomica.species.SpeciesOriented
-
- init() - Method in class etomica.thermointegration.LjMc3D.Applet
-
- init() - Method in class etomica.veos.bigdecimal.Wigner3jGUI
-
- init() - Method in class etomica.virial.cluster.VirialDiagrams
-
- init() - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- init() - Method in class etomica.virial.simulations.SimulationVirial
-
- init() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- init() - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- init() - Method in class etomica.virial.SpeciesFactorySpheres2
-
- initAlpha() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- initAlpha() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- initAlpha() - Method in class etomica.normalmode.MeterOverlapSwitch
-
- initAlpha() - Method in class etomica.normalmode.MeterTargetTP
-
- initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage
-
- initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- initBennettParameter(String, int, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- initBlockAccumulator() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- initBox(Box) - Method in class etomica.normalmode.P1ConstraintNbr
-
Assigns & keeps track of a set of neighbors for each box
- initC - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
-
- initCar - Variable in class etomica.modules.render.RenderMD.RenderMDParam
-
- initCellEditor(TableModel) - Method in class etomica.graphics.DeviceTable
-
- initComponents() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- initComponents() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- initHistogram(int, IDataSink) - Method in class etomica.data.AccumulatorAverageBootstrap
-
- initialize() - Method in class etomica.association.AssociationManager
-
- initialize() - Method in class etomica.association.AssociationManagerMolecule
-
- initialize() - Method in class etomica.graphics.DisplayPolytopeCanvas2D
-
- initialize(long) - Method in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- initialize(long) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- initialize(long) - Method in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- initialize(long) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- initialize(long) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- initialize(long) - Method in class etomica.normalmode.SimEinStep2
-
- initialize(long) - Method in class etomica.normalmode.SimEinStep2HCP
-
- initialize(long) - Method in class etomica.normalmode.SimLJHTTISuper
-
- initialize(long) - Method in class etomica.normalmode.SimLJHTTISuperHCP
-
- initialize(long) - Method in class etomica.normalmode.SimOverlapSoftSphereDP
-
- initialize(long) - Method in class etomica.normalmode.SimOverlapSoftSphereEin
-
- initialize(long) - Method in class etomica.normalmode.SimOverlapSoftSphereTP
-
- initialize(long) - Method in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- initialize(long) - Method in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- initialize() - Method in class etomica.potential.P2QChemInterpolated
-
- initialize(Bootstrap<EtomicaServerConfig>) - Method in class etomica.server.EtomicaServer
-
- initialize(ApiPlatform) - Method in class org.jmol.g3d.Graphics3D
-
- initialize(ApiPlatform) - Method in class org.jmol.util.GData
-
- initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
-
- initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
-
- initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
-
- initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- initializeConfigFromFile(String) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- initializeConfigFromFile(String) - Method in class etomica.normalmode.SimFluidSoftSphere
-
- initializeConfiguration(String) - Method in class etomica.dimer.SimDimerLJadatom
-
- initializeConfiguration(String) - Method in class etomica.dimer.SimDimerMEAMadatom
-
- initializeConfiguration(String) - Method in class etomica.dimer.SimDimerMEAMGB
-
- initializeConfiguration(String) - Method in class etomica.kmc.SimKMCLJadatom
-
- initializeConfiguration(String) - Method in class etomica.kmc.SimKMCMEAMadatom
-
- initializeConformation(IMolecule, Vector) - Method in class etomica.models.nitrogen.SpeciesN2
-
- initializeConformation(IMolecule) - Method in interface etomica.species.ISpecies
-
Initializes the molecule's IAtoms in their standard arrangement.
- initializeConformation(IMolecule) - Method in class etomica.species.Species
-
- initializeCoordinates() - Method in class etomica.action.IntegratorDimerApproach
-
- initializeCoordinates(Box) - Method in interface etomica.config.Configuration
-
Defines the placement of the molecules.
- initializeCoordinates(Box) - Method in class etomica.config.ConfigurationFile
-
- initializeCoordinates(Box) - Method in class etomica.config.ConfigurationFileBinary
-
- initializeCoordinates(Box) - Method in class etomica.config.ConfigurationLattice
-
Places the molecules in the given box on the positions of the
lattice.
- initializeCoordinates(Box, ISpecies) - Method in class etomica.config.ConfigurationLattice
-
- initializeCoordinates(Box) - Method in class etomica.config.ConfigurationLatticeSimple
-
Places the molecules in the given box on the positions of the
lattice.
- initializeCoordinates(Box) - Method in class etomica.config.ConfigurationLatticeWithPlane
-
Places the molecules in the given box on the positions of the
lattice.
- initializeCoordinates(Box) - Method in class etomica.config.ConfigurationResourceFile
-
- initializeCoordinates(Box) - Method in class etomica.config.ConfigurationZincblende
-
Initializes positions of atoms to the zincblende structure.
- initializeCoordinates(Box) - Method in class etomica.config.GrainBoundaryConfiguration
-
Places the molecules in the given box on the positions of the
lattice.
- initializeCoordinates(Box) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
- initializeCoordinates(Box) - Method in class etomica.interfacial.ConfigurationLammps
-
- initializeCoordinates(int[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- initializeCoordinates(int[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- initializeCoordinates(Box) - Method in class etomica.models.water.ConfigurationFileTIP4P
-
- initializeCoordinates(Box) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- initializeCoordinates(Box) - Method in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
-
Places the molecules in the given box on the positions of the
lattice.
- initializeCoordinates(Box) - Method in class etomica.modules.chainequilibrium.ConfigurationLatticeRandom
-
- initializeCoordinates(Box) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- initializeCoordinates(Box) - Method in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
-
- initializeCoordinates(Box) - Method in class etomica.modules.droplet.ConfigurationDroplet
-
- initializeCoordinates(Box) - Method in class etomica.modules.entropylottery.ConfigurationZero
-
- initializeCoordinates(Box) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- initializeCoordinates(Box) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- initializeCoordinates(Box) - Method in class etomica.modules.sam.ConfigurationSAM
-
- initializeCoordinates(int[]) - Method in class etomica.normalmode.CoordinateDefinition
-
- initializeCoordinates(int[]) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- initializeCoordinates(int[]) - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- initializeCoordinates(int[]) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
-
- initializeCoordinates(int[]) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- initializeCoordinates(Box) - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
Places the molecules in the given box on the positions of the
lattice.
- initializeCoordinates(Box) - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
Places the molecules in the given box on the positions of the
lattice.
- initializeCoordinates(int[]) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- initializeCoordinates(Box) - Method in class etomica.rotation.ConfigurationWater108
-
- initializeCoordinates(Box) - Method in class etomica.rotation.ConfigurationWater108TIP4P
-
- initializeCoordinates(Box) - Method in class etomica.rotation.ConfigurationWater256
-
- initializeCoordinates(Box) - Method in class etomica.rotation.ConfigurationWater3
-
- initializeCoordinates(Box) - Method in class etomica.rotation.ConfigurationWater3_3P
-
- initializeCoordinates(Box) - Method in class etomica.spin.ConfigurationAligned
-
Sets all spins to be aligned in the +x direction
- initializeCoordinates(Box) - Method in class etomica.virial.ConfigurationCluster
-
- initializeCoordinates(Box, boolean, boolean) - Method in class etomica.virial.ConfigurationClusterAceticAcid
-
- initializeCoordinates(Box) - Method in class etomica.virial.ConfigurationClusterChain
-
- initializeCoordinates(Box) - Method in class etomica.virial.ConfigurationClusterChainFourSites
-
- initializeCoordinates(Box) - Method in class etomica.virial.ConfigurationClusterMove
-
- initializeCoordinates(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- initializeCoordinates(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- initializeCoordinates(Box) - Method in class etomica.zeolite.ConfigurationFileXYZ
-
- initializeCoordinates2(Box, boolean, boolean) - Method in class etomica.virial.ConfigurationClusterAceticAcid
-
- initializeCoordinates2(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- initializeCoordinates2(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- initializeCoordinates3(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- initializeCoordinates3(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- initializeCoordinates4(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- initializeCoordinates4(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- initializeCoordinates4Mol(Box, char, char, char, char, char, int, int) - Method in class etomica.virial.ConfigurationClusterAceticAcid
-
- initializeCoordinates5(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- initializeCoordinates5(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- initializeCoordinatesBranch(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- initializeCoordinatesER(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- initializeCoordinatesER(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- initializeCoordinatesRef(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- initializeCoordinatesTetramer(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- initializeCoordinatesTrimer(Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- initialized - Variable in class etomica.integrator.Integrator
-
- initialized() - Method in class etomica.integrator.IntegratorEventManager
-
- initialized - Variable in class etomica.models.water.OrientationCalcWater3P
-
- initialized - Variable in class etomica.models.water.OrientationCalcWater4P
-
- initialized - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- initialized - Variable in class etomica.nbr.list.NeighborListManager
-
- initialized - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- InitializeMolecules(ConfigurationLatticeWithPlane, SimulationRestart) - Constructor for class etomica.modules.osmosis.Osmosis.InitializeMolecules
-
- initializePositions(IAtomList) - Method in class etomica.AlkaneEH.ConformationAlkaneEH
-
- initializePositions(IAtomList) - Method in class etomica.AlkaneEH.ConformationMethane
-
- initializePositions(IAtomList) - Method in class etomica.config.ConformationChain
-
Places a set of atoms in a linearly connected fashion.
- initializePositions(IAtomList) - Method in class etomica.config.ConformationChainLinear
-
- initializePositions(IAtomList) - Method in class etomica.config.ConformationGeneric
-
- initializePositions(IAtomList) - Method in class etomica.config.ConformationLinear
-
- initializePositions(IAtomList) - Method in class etomica.config.ConformationWater
-
- initializePositions(IAtomList) - Method in interface etomica.config.IConformation
-
Defined by subclass to assign coordinates to the atoms in the given list.
- initializePositions(IAtomList, IOrientation) - Method in interface etomica.config.IConformationOriented
-
Assign coordinates to the atoms in the given list using the
given orientation for the molecule.
- initializePositions(IAtomList) - Method in class etomica.models.nitrogen.ConformationNitrogen
-
- initializePositions(IAtomList, Vector) - Method in class etomica.models.nitrogen.ConformationNitrogen
-
- initializePositions(IAtomList) - Method in class etomica.models.nitrogen.ConformationNitrogenShellModel
-
- initializePositions(IAtomList) - Method in class etomica.models.OPLS.ConformationAceticAcid
-
- initializePositions(IAtomList) - Method in class etomica.models.rowley.ConformationEthanol
-
- initializePositions(IAtomList) - Method in class etomica.models.rowley.ConformationMethanol
-
- initializePositions(IAtomList) - Method in class etomica.models.traPPE.ConformationMethanol
-
- initializePositions(IAtomList) - Method in class etomica.models.water.ConformationWater3P
-
- initializePositions(IAtomList) - Method in class etomica.models.water.ConformationWaterGCPM
-
- initializePositions(IAtomList) - Method in class etomica.models.water.ConformationWaterGCPMCOM
-
- initializePositions(IAtomList) - Method in class etomica.models.water.ConformationWaterTIP4P
-
- initializePositions(IAtomList) - Method in class etomica.models.water.OrientationCalcWater3P
-
- initializePositions(IAtomList) - Method in class etomica.models.water.OrientationCalcWater4P
-
- initializePositions(IAtomList) - Method in class etomica.modules.dcvgcmd.ConformationTube
-
- initializePositions(IAtomList) - Method in class etomica.modules.rheology.ConformationPolymer
-
- initializePositions(IAtomList, IOrientation) - Method in class etomica.normalmode.ConformationHSDimer
-
- initializePositions(IAtomList) - Method in class etomica.normalmode.ConformationHSDimer
-
- initializePositions(IAtomList) - Method in class etomica.paracetamol.ConformationParacetamol
-
- initializePositions(IAtomList) - Method in class etomica.paracetamol.ConformationParacetamolMonoclinic
-
- initializePositions(IAtomList) - Method in class etomica.paracetamol.ConformationParacetamolOrthorhombic
-
- initializePositions(IAtomList) - Method in class etomica.virial.Conformation7SiteRigidSF6
-
- initializePositions(IAtomList) - Method in class etomica.virial.ConformationAnthracene3site
-
- initializePositions(IAtomList) - Method in class etomica.virial.ConformationAnthraceneTraPPE
-
- initializePositions(IAtomList) - Method in class etomica.virial.ConformationCO2
-
- initializePositions(IAtomList) - Method in class etomica.virial.ConformationMethane
-
- initializePositions(IAtomList) - Method in class etomica.virial.ConformationNaphthaleneTraPPE
-
- initializePositions(IAtomList) - Method in class etomica.virial.ConformationPh3site
-
- initializePositions(IAtomList) - Method in class etomica.virial.ConformationPhenanthreneTraPPE
-
- initializeSim() - Method in class etomica.threads.AtomDecompositionMD
-
- initializing - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- initializing - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
-
- initialLatticeEnergy - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- initialSeed - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- initialSeed - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- initialSolute - Static variable in class etomica.modules.osmosis.OsmosisSim
-
- initialSolvent - Static variable in class etomica.modules.osmosis.OsmosisSim
-
- initialState(Graph, Graph) - Static method in class etomica.graph.isomorphism.Match
-
Initial search state with the default isomorphism test algorithm.
- initialU - Static variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- initialU - Static variable in class etomica.models.clathrates.MinimizationTIP4P
-
- initialU - Static variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- initLat - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- initMetaDataComparator() - Static method in class etomica.virial.cluster.VirialDiagrams
-
- initMetaDataComparator() - Static method in class etomica.virial.cluster.VirialDiagramsPT
-
- initMolecOrientation - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- initMolecOrientation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- initMolecOrientation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- initMolecOrientation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- initNominalU(IMoleculeList) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
-
- initNominalU(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
Override if nominal U is more than the lattice position of the molecule
Number of molecules equals to basis atoms
initNomial is the method to define the initial orientation of the molecule
- initNominalU(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
Override if nominal U is more than the lattice position of the molecule
Number of molecules equals to basis atoms
initNomial is the method to define the initial orientation of the molecule
- initNominalU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinition
-
Initializes the CoordinateDefinition for the given molecule and
associates the molecule with the given index.
- initNominalU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionLeaf
-
- initNominalU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
-
Override if nominal U is more than the lattice position of the molecule
- initNominalU(IMoleculeList) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
Override if nominal U is more than the lattice position of the molecule
- initNominalU(IMoleculeList) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
Override if nominal U is more than the lattice position of the molecule
- initP() - Method in class etomica.normalmode.MeterDDP
-
- initP() - Method in class etomica.normalmode.MeterDP
-
- initPotential(Space, SpeciesAceticAcid, PotentialGroup) - Static method in class etomica.models.OPLS.AceticAcidModPotentialHelper
-
- initPotential(Space, SpeciesAceticAcid, PotentialGroup) - Static method in class etomica.models.OPLS.AceticAcidPotentialHelper
-
- initPotential(Space, SpeciesEthanol, PotentialGroup, boolean) - Static method in class etomica.models.rowley.EthanolPotentialHelper
-
- initPotential(Space, SpeciesMethanol, PotentialGroup, boolean, double, double) - Static method in class etomica.models.rowley.MethanolPotentialHelper
-
- initPotential(Space, SpeciesMethanol, PotentialGroup) - Static method in class etomica.models.traPPE.MethanolPotentialHelper
-
- initPotentials(Simulation) - Method in class etomica.chem.models.Model
-
Internal method to be implemented by subclasses to initialize the
intramolecular potentials associated with this model.
- initPotentials(Simulation) - Method in class etomica.chem.models.ModelChain
-
- initRefPref(String, long) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- initRefPref(String, long) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- initRefPref(String, long, int) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- initRefPref(String, long) - Method in class etomica.normalmode.SimOverlap
-
- initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapLJ
-
- initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapModule
-
- initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphere
-
- initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- initRefPref(String, long) - Method in class etomica.normalmode.SimOverlapSSnxy
-
- initRefPref(String, long) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- initRefPref(String, long) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- initRefPref(String, long) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- initU - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- initU - Variable in class etomica.models.nitrogen.MeterDirectInitPert
-
- initVolume - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
-
- initVolume - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- innersegment - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- inPlane(Vector) - Method in class etomica.lattice.LatticePlane
-
Returns true if the given point is inside the plane (within some small tolerance).
- inPlane(Vector) - Method in class etomica.math.geometry.Plane
-
Returns true if the given point is within a distance epsilon of this plane.
- inputDataInfo - Variable in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- inputFile - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- inputFile - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- inputFile - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- inputfilename - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- inputfilename - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- inputfilename - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- inputfilename - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- inputfilename - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- inputfilename - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- inputfilename - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- inputfilename - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
-
- inputfilename - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- inputfilename - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
-
- inRadius - Variable in class etomica.atom.AtomTypeSpheroPolyhedron
-
- insert - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- insertCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- insertCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- inserted - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- inserted - Variable in class etomica.virial.MCMoveClusterAtomHSTree
-
- inserted - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
-
- Insertion - Class in etomica.modules.insertion
-
- Insertion(Space) - Constructor for class etomica.modules.insertion.Insertion
-
- insertion - Static variable in class org.jmol.script.Token
-
- InsertionGraphic - Class in etomica.modules.insertion
-
- InsertionGraphic(Insertion, Space) - Constructor for class etomica.modules.insertion.InsertionGraphic
-
- InsertionGraphic.Applet - Class in etomica.modules.insertion
-
- InsertionGraphic.MeterWidom - Class in etomica.modules.insertion
-
- INSTANCE - Static variable in class etomica.atom.iterator.AtomIteratorNull
-
- INSTANCE - Static variable in class etomica.chem.elements.Argon
-
- INSTANCE - Static variable in class etomica.chem.elements.Carbon
-
- INSTANCE - Static variable in class etomica.chem.elements.Chlorine
-
- INSTANCE - Static variable in class etomica.chem.elements.Copper
-
- INSTANCE - Static variable in class etomica.chem.elements.Fluorine
-
- INSTANCE - Static variable in class etomica.chem.elements.Helium
-
- INSTANCE - Static variable in class etomica.chem.elements.Hydrogen
-
- INSTANCE - Static variable in class etomica.chem.elements.Iron
-
- INSTANCE - Static variable in class etomica.chem.elements.Nitrogen
-
- INSTANCE - Static variable in class etomica.chem.elements.Oxygen
-
- INSTANCE - Static variable in class etomica.chem.elements.Silver
-
- INSTANCE - Static variable in class etomica.chem.elements.Sodium
-
- INSTANCE - Static variable in class etomica.chem.elements.Sulfur
-
- INSTANCE - Static variable in class etomica.chem.elements.Tin
-
- INSTANCE - Static variable in class etomica.chem.elements.Tungsten
-
- INSTANCE - Static variable in class etomica.math.function.Function.Abs
-
- INSTANCE - Static variable in class etomica.math.function.Function.Exp
-
- INSTANCE - Static variable in class etomica.math.function.Function.Identity
-
- INSTANCE - Static variable in class etomica.math.function.Function.Log
-
- INSTANCE - Static variable in class etomica.math.function.Function.Reciprocal
-
- INSTANCE - Static variable in class etomica.math.function.Function.Sqrt
-
- INSTANCE - Static variable in class etomica.molecule.iterator.IteratorFactory
-
- INSTANCE - Static variable in class etomica.paracetamol.HydrogenP
-
- InstanceProperty - Class in etomica.meta.properties
-
Container class for mapping an instance to a property.
- InstanceProperty(Object, PropertyDescriptor) - Constructor for class etomica.meta.properties.InstanceProperty
-
- Int - Class in etomica.graph.operations
-
- Int() - Constructor for class etomica.graph.operations.Int
-
- Int2IntHash - Class in org.jmol.util
-
- Int2IntHash(int) - Constructor for class org.jmol.util.Int2IntHash
-
- intArrayList - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- intArrayList - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- integer - Static variable in class org.jmol.script.Token
-
- integral(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- integral(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
- integral(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
- integral(double) - Method in class etomica.potential.P2Ideal
-
Returns zero.
- integral(double) - Method in class etomica.potential.P2LJQ
-
- integral(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
-
- integral(double) - Method in class etomica.potential.P2SoftTruncated
-
Returns the value of uInt for the wrapped potential.
- integral(double) - Method in interface etomica.potential.Potential2Soft
-
Integral used to evaluate correction to truncation of potential.
- integral(double) - Method in class etomica.potential.Potential2SoftSpherical
-
Same as uInt.
- integrand(double) - Method in class etomica.statmech.HardSphere
-
- integrate(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Replaces each cluster in the given array with another having the same
topology, but with the highest-index root point converted into a field
point.
- integrator - Variable in class etomica.action.IntegratorActionAdapter
-
- integrator - Variable in class etomica.AlkaneEH.CH4NVT
-
- integrator - Variable in class etomica.AlkaneEH.DHS_NVT
-
- integrator - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
-
- integrator - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- integrator - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- integrator - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- integrator - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- integrator - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- integrator - Variable in class etomica.data.DataProcessorChemicalPotential
-
- integrator - Variable in class etomica.data.DataSourceCountCollisions
-
- integrator - Variable in class etomica.data.DataSourceCountSteps
-
- integrator - Variable in class etomica.data.DataSourceCountTime
-
- integrator - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
-
- integrator - Variable in class etomica.data.meter.MeterPressureTensorFromIntegrator
-
- integrator - Variable in class etomica.densityofstate.DensityOfState
-
- integrator - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
-
- integrator - Variable in class etomica.dielectric.DHS_NVT
-
- integrator - Variable in class etomica.dielectric.DLJ_NVT_1site
-
- integrator - Variable in class etomica.dielectric.TIP4P_NVT
-
- integrator - Variable in class etomica.freeenergy.npath.SimFe
-
- integrator - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- integrator - Variable in class etomica.freeenergy.npath.SimLJ
-
- integrator - Variable in class etomica.graphics.DisplayTimer
-
- Integrator - Class in etomica.integrator
-
Integrator implements the algorithm used to move the atoms around and
generate new configurations in one or more boxs.
- Integrator() - Constructor for class etomica.integrator.Integrator
-
- integrator - Variable in class etomica.integrator.IntegratorHard.Agent
-
- integrator - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- integrator - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- integrator - Variable in class etomica.interfacial.LJMC
-
- integrator - Variable in class etomica.interfacial.LJMD
-
- integrator - Variable in class etomica.liquidLJ.LjMC3D
-
- integrator - Variable in class etomica.liquidLJ.LjMd3D
-
- integrator - Variable in class etomica.liquidLJ.LjMd3D.ValueCache
-
- integrator - Variable in class etomica.liquidLJ.ValueCache
-
- integrator - Variable in class etomica.mappedRdf.MappedRdf
-
- integrator - Variable in class etomica.mappedvirial.MappedU
-
- integrator - Variable in class etomica.mappedvirial.MappedVirialLJ
-
- integrator - Variable in class etomica.mappedvirial.MappedVirialLJVGr
-
- integrator - Variable in class etomica.meam.EFSTungsten
-
- integrator - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- integrator - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- integrator - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- integrator - Variable in class etomica.meam.MEAM_MC
-
- integrator - Variable in class etomica.meam.MEAMMd3D
-
- integrator - Variable in class etomica.metastable.LJmuVT
-
- integrator - Variable in class etomica.metastable.LJNPT
-
- integrator - Variable in class etomica.metastable.LJNVT
-
- integrator - Variable in class etomica.models.hexane.HexaneVolumeFraction
-
- integrator - Variable in class etomica.models.hexane.SimHarmonicHexane
-
- integrator - Variable in class etomica.models.hexane.TestHexane
-
- integrator - Variable in class etomica.models.hexane.TestHexaneCBMCOnly
-
- integrator - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- integrator - Variable in class etomica.models.hexane.TestHexaneHarmonic
-
- integrator - Variable in class etomica.models.hexane.TestSetToUHexane
-
- integrator - Variable in class etomica.models.nitrogen.MeterBoltzmann
-
- integrator - Variable in class etomica.models.nitrogen.MeterBoltzmannDirect
-
- integrator - Variable in class etomica.models.nitrogen.MeterDirectInitPert
-
- integrator - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- integrator - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- integrator - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- integrator - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- integrator - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- integrator - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- integrator - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- integrator - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- integrator - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- integrator - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
-
- integrator - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
-
- integrator - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
-
- integrator - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
-
- integrator - Variable in class etomica.models.oneDHardRods.SimWidomMode
-
- integrator - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- integrator - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- integrator - Variable in class etomica.models.water.TestEwaldTIP4PWater
-
- integrator - Variable in class etomica.modules.adsorption.ModifierPMu
-
- integrator - Variable in class etomica.modules.adsorption.P1Wall
-
- integrator - Variable in class etomica.modules.catalysis.Catalysis
-
- integrator - Variable in class etomica.modules.colloid.ColloidSim
-
- integrator - Variable in class etomica.modules.droplet.Droplet
-
- integrator - Variable in class etomica.modules.droplet.DropletAtomic
-
- integrator - Variable in class etomica.modules.ensembles.LJMC
-
- integrator - Variable in class etomica.modules.entropylottery.EntropyLottery
-
- integrator - Variable in class etomica.modules.insertion.Insertion
-
- integrator - Variable in class etomica.modules.interfacial.InterfacialSW
-
- integrator - Variable in class etomica.modules.ljmd.Ljmd
-
- integrator - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- integrator - Variable in class etomica.modules.mu.Mu
-
- integrator - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
-
- integrator - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- integrator - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- integrator - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
-
- integrator - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- integrator - Variable in class etomica.modules.osmosis.OsmosisSim
-
- integrator - Variable in class etomica.modules.pistoncylinder.PistonCylinder
-
- integrator - Variable in class etomica.modules.render.RenderMD
-
The Integrator performing the dynamics.
- integrator - Variable in class etomica.modules.rheology.MeterNormalStress
-
- integrator - Variable in class etomica.modules.rheology.MeterViscosity
-
- integrator - Variable in class etomica.modules.rheology.SimulationRheology
-
- integrator - Variable in class etomica.modules.rosmosis.MeterFlux
-
- integrator - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- integrator - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- integrator - Variable in class etomica.modules.sam.Sam
-
- integrator - Variable in class etomica.modules.statistics.AccumulatorMimicMu
-
- integrator - Variable in class etomica.modules.statistics.DataProcessorMu
-
- integrator - Variable in class etomica.modules.swmd.Swmd
-
- integrator - Variable in class etomica.normalmode.DeviceEigenvaluesSlider
-
- integrator - Variable in class etomica.normalmode.DeviceWaveVectorSlider
-
- integrator - Variable in class etomica.normalmode.HessianDB
-
- integrator - Variable in class etomica.normalmode.HSDimerNPT
-
- integrator - Variable in class etomica.normalmode.HSNPT
-
- integrator - Variable in class etomica.normalmode.HTTPSoftSphereSim
-
- integrator - Variable in class etomica.normalmode.MeterBoltzmann
-
- integrator - Variable in class etomica.normalmode.MeterDirectSamplingTarget
-
- integrator - Variable in class etomica.normalmode.MeterSamplingHarmonic
-
- integrator - Variable in class etomica.normalmode.MeterSamplingTarget
-
- integrator - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
-
- integrator - Variable in class etomica.normalmode.MeterWorkBennetTarget
-
- integrator - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- integrator - Variable in class etomica.normalmode.MeterWorkTargetBennet
-
- integrator - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- integrator - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- integrator - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
-
- integrator - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- integrator - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- integrator - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- integrator - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- integrator - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- integrator - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- integrator - Variable in class etomica.normalmode.SimBennet
-
- integrator - Variable in class etomica.normalmode.SimCalcJ
-
- integrator - Variable in class etomica.normalmode.SimCalcS
-
- integrator - Variable in class etomica.normalmode.SimCalcSLJ
-
- integrator - Variable in class etomica.normalmode.SimCalcSMorse
-
- integrator - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
-
- integrator - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- integrator - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- integrator - Variable in class etomica.normalmode.SimEinStep1
-
- integrator - Variable in class etomica.normalmode.SimEinStep1HCP
-
- integrator - Variable in class etomica.normalmode.SimEinStep2
-
- integrator - Variable in class etomica.normalmode.SimEinStep2HCP
-
- integrator - Variable in class etomica.normalmode.SimFluidSoftSphere
-
- integrator - Variable in class etomica.normalmode.SimHarmonic
-
- integrator - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- integrator - Variable in class etomica.normalmode.SimHSMDVacancy
-
- integrator - Variable in class etomica.normalmode.SimLJHTTISuper
-
- integrator - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- integrator - Variable in class etomica.normalmode.SimLJVacancy
-
- integrator - Variable in class etomica.normalmode.SimModesJ
-
- integrator - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- integrator - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- integrator - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- integrator - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- integrator - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- integrator - Variable in class etomica.normalmode.SimTarget
-
- integrator - Variable in class etomica.normalmode.SimTargetUmbrella
-
- integrator - Variable in class etomica.normalmode.SimUmbrella
-
- integrator - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- integrator - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- integrator - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- integrator - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- integrator - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- integrator - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
-
The Integrator performing the dynamics.
- integrator - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
-
The Integrator performing the dynamics.
- integrator - Variable in class etomica.potential.PotentialCalculationPressureTensor
-
- integrator - Variable in class etomica.rotation.DipoleBox
-
- integrator - Variable in class etomica.rotation.DipoleBoxMatrix
-
- integrator - Variable in class etomica.simulation.prototypes.ChainHSMD3D
-
- integrator - Variable in class etomica.simulation.prototypes.GEMCWithRotation
-
- integrator - Variable in class etomica.simulation.prototypes.HSMC2D
-
- integrator - Variable in class etomica.simulation.prototypes.HSMD2D
-
- integrator - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- integrator - Variable in class etomica.simulation.prototypes.HSMD3D
-
The Integrator performing the dynamics.
- integrator - Variable in class etomica.simulation.prototypes.HSMD3DNoNbr
-
- integrator - Variable in class etomica.simulation.prototypes.LJMD2D
-
- integrator - Variable in class etomica.simulation.prototypes.LJMD3D
-
- integrator - Variable in class etomica.simulation.prototypes.SoftSphere3d
-
- integrator - Variable in class etomica.simulation.prototypes.SWMD2D
-
- integrator - Variable in class etomica.simulation.prototypes.SWMD3D
-
- integrator - Variable in class etomica.surfacetension.LJMC
-
- integrator - Variable in class etomica.tests.TestHSMD3D
-
- integrator - Variable in class etomica.tests.TestLJGCMC3D
-
- integrator - Variable in class etomica.tests.TestLJMC3D
-
- integrator - Variable in class etomica.tests.TestSWChain
-
- integrator - Variable in class etomica.thermointegration.LjMc3D
-
- integrator - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- integrator - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- integrator - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- integrator - Variable in class etomica.virial.simulations.ModifierTPI
-
- integrator - Variable in class etomica.virial.simulations.SimulationVirial
-
- integrator - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- integrator - Variable in class etomica.yukawa.TestHC2YukawaMC3D
-
- integrator - Variable in class etomica.yukawa.TestYukawaMC3D
-
- integrator - Variable in class etomica.yukawa.TestYukawaMD3D
-
- integrator - Variable in class etomica.zeolite.ZeoliteSimulation
-
The Integrator performing the dynamics.
- Integrator.Forcible - Interface in etomica.integrator
-
Integrator agent that holds a force vector.
- Integrator.Torquable - Interface in etomica.integrator
-
Integrator agent that holds a torque vector.
- integrator1 - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- integrator1 - Variable in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- integrator2 - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- integrator2 - Variable in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- integrator3 - Variable in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- integratorA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- integratorA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- integratorA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- integratorA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- IntegratorAction - Interface in etomica.action
-
Elementary action performed on an integrator.
- IntegratorActionAdapter - Class in etomica.action
-
Convenience class used to define a IntegratorAction.
- IntegratorActionAdapter() - Constructor for class etomica.action.IntegratorActionAdapter
-
- IntegratorActionAdapter(Integrator) - Constructor for class etomica.action.IntegratorActionAdapter
-
Constructs the Action with the given descriptive label.
- integratorAgentManager - Variable in class etomica.potential.PotentialCalculationForceSum
-
- IntegratorAnalytic - Class in etomica.integrator
-
Integrator that generates atom trajectories from an analytic formula.
- IntegratorAnalytic(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.IntegratorAnalytic
-
- IntegratorAnalytic(PotentialMaster, IRandom, double, Space) - Constructor for class etomica.integrator.IntegratorAnalytic
-
- IntegratorAnalytic.AtomTimeAction - Class in etomica.integrator
-
Extends AtomAction class to add a method to set the time.
- integratorB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- integratorB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- integratorB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- integratorB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- IntegratorBox - Class in etomica.integrator
-
Superclass of integrators that acts on a single box.
- IntegratorBox(PotentialMaster, double) - Constructor for class etomica.integrator.IntegratorBox
-
- IntegratorConNVT - Class in etomica.integrator
-
Constant NVT Molecular Dynamics Integrator-Constraint Method
Uses a modified version of the Leap Frog Algorithm.
- IntegratorConNVT(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.IntegratorConNVT
-
- IntegratorConNVT(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.integrator.IntegratorConNVT
-
- IntegratorConNVT.Agent - Class in etomica.integrator
-
- integratorDCV - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- IntegratorDCVGCMD - Class in etomica.modules.dcvgcmd
-
- IntegratorDCVGCMD(PotentialMaster, double, Space, ISpecies, ISpecies) - Constructor for class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- IntegratorDCVGCMD.Mu1Modulator - Class in etomica.modules.dcvgcmd
-
- IntegratorDCVGCMD.Mu2Modulator - Class in etomica.modules.dcvgcmd
-
- integratorDimer - Variable in class etomica.dimer.SimDimerLJadatom
-
- integratorDimer - Variable in class etomica.dimer.SimDimerLJgb
-
- integratorDimer - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- integratorDimer - Variable in class etomica.dimer.SimDimerMEAMGB
-
- integratorDimer - Variable in class etomica.kmc.SimKMCLJadatom
-
- integratorDimer - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- IntegratorDimerApproach - Class in etomica.action
-
- IntegratorDimerApproach(PotentialMaster, Space) - Constructor for class etomica.action.IntegratorDimerApproach
-
- IntegratorDimerMin - Class in etomica.dimer
-
Henkelman's Dimer Method (Minimum Energy Path).
- IntegratorDimerMin(Simulation, PotentialMaster, ISpecies[], Boolean, Space) - Constructor for class etomica.dimer.IntegratorDimerMin
-
- IntegratorDimerMin(Simulation, PotentialMaster, double, ISpecies[], Boolean, Space) - Constructor for class etomica.dimer.IntegratorDimerMin
-
- integratorDimerMin - Variable in class etomica.dimer.SimDimerLJadatom
-
- integratorDimerMin - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- integratorDimerMin - Variable in class etomica.dimer.SimDimerMEAMGB
-
- IntegratorDimerRT - Class in etomica.dimer
-
Henkelman's Dimer Method (Rotation and Translation).
- IntegratorDimerRT(Simulation, PotentialMaster, ISpecies[], Space) - Constructor for class etomica.dimer.IntegratorDimerRT
-
- IntegratorDimerRT(Simulation, PotentialMaster, IRandom, double, ISpecies[], Space) - Constructor for class etomica.dimer.IntegratorDimerRT
-
- IntegratorDroplet - Class in etomica.modules.droplet
-
Mesoscale integrator for Droplet module.
- IntegratorDroplet(Simulation, PotentialMaster, Space) - Constructor for class etomica.modules.droplet.IntegratorDroplet
-
- IntegratorDroplet(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.modules.droplet.IntegratorDroplet
-
- IntegratorDroplet.MyAgent - Class in etomica.modules.droplet
-
- IntegratorEnergyMap - Class in etomica.dimer
-
- IntegratorEnergyMap(Simulation, PotentialMaster, IAtom, String, Space) - Constructor for class etomica.dimer.IntegratorEnergyMap
-
- IntegratorEvent - Class in etomica.integrator
-
- IntegratorEvent(Integrator) - Constructor for class etomica.integrator.IntegratorEvent
-
- IntegratorEventManager - Class in etomica.integrator
-
- IntegratorEventManager(Integrator) - Constructor for class etomica.integrator.IntegratorEventManager
-
- IntegratorFixedWall - Class in etomica.interfacial
-
- IntegratorFixedWall(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.interfacial.IntegratorFixedWall
-
- integratorForceComputed(IntegratorEvent) - Method in interface etomica.integrator.IntegratorListenerMD
-
Invoked after the integrator has computed the forces on all atoms
in the system.
- integratorForceComputed(IntegratorEvent) - Method in class etomica.interfacial.FixedWall
-
- integratorForcePrecomputed(IntegratorEvent) - Method in interface etomica.integrator.IntegratorListenerMD
-
Invoked before the integrator computes the forces on all atoms
in the system.
- integratorForcePrecomputed(IntegratorEvent) - Method in class etomica.interfacial.FixedWall
-
- IntegratorGear4 - Class in etomica.integrator
-
Gear 4th-order predictor-corrector integrator.
- IntegratorGear4(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.IntegratorGear4
-
- IntegratorGear4(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.integrator.IntegratorGear4
-
- IntegratorGear4.Agent - Class in etomica.integrator
-
- IntegratorGear4NPH - Class in etomica.integrator
-
Gear 4th-order predictor-corrector integrator for constant enthalphy, pressure.
- IntegratorGear4NPH(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.IntegratorGear4NPH
-
- IntegratorGear4NPH(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.integrator.IntegratorGear4NPH
-
- IntegratorGear4NPH.EnsembleToggler - Class in etomica.integrator
-
- IntegratorGear4NPH.ForceSumNPH - Class in etomica.integrator
-
- IntegratorGear4NPH.MeterEnthalpy - Class in etomica.integrator
-
- IntegratorGEMC - Class in etomica.integrator
-
Simple Gibbs-ensemble Monte Carlo integrator.
- IntegratorGEMC(IRandom, Space) - Constructor for class etomica.integrator.IntegratorGEMC
-
- integratorGEMC - Variable in class etomica.modules.vle.VLESim
-
- integratorHard - Variable in class etomica.data.DataSourceTensorVirialHard
-
- integratorHard - Variable in class etomica.data.meter.MeterPressureHard
-
- IntegratorHard - Class in etomica.integrator
-
Integrator for hard potentials.
- IntegratorHard(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.IntegratorHard
-
- IntegratorHard(Simulation, PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.integrator.IntegratorHard
-
- integratorHard - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- integratorHard - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- integratorHard - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- integratorHard - Variable in class etomica.modules.mu.DataSourceWallPressureMu
-
- IntegratorHard.Agent - Class in etomica.integrator
-
Agent defined by this integrator.
- IntegratorHard.CollisionHandlerUp - Class in etomica.integrator
-
- IntegratorHard.CollisionListener - Interface in etomica.integrator
-
- integratorHard1 - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- IntegratorHardMDMC - Class in etomica.normalmode
-
Custom DMD integrator that handles hybrid simulations with
insertion/deletions.
- IntegratorHardMDMC(Simulation, PotentialMaster, Space) - Constructor for class etomica.normalmode.IntegratorHardMDMC
-
- IntegratorHardPiston - Class in etomica.modules.pistoncylinder
-
Integrator for DMD with a piston (P1HardMovingBoundary)
- IntegratorHardPiston(Simulation, PotentialMaster, P1HardMovingBoundary, Space) - Constructor for class etomica.modules.pistoncylinder.IntegratorHardPiston
-
- integratorHarmonic - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- IntegratorHarmonic - Class in etomica.normalmode
-
Integrator that is used for the harmonic osciallating system
- IntegratorHarmonic(IRandom, double, double, Space) - Constructor for class etomica.normalmode.IntegratorHarmonic
-
- integratorHybrid - Variable in class etomica.modules.adsorption.Adsorption
-
- IntegratorHybrid - Class in etomica.modules.adsorption
-
- IntegratorHybrid(PotentialMasterHybrid, IntegratorMD, IntegratorMC, double) - Constructor for class etomica.modules.adsorption.IntegratorHybrid
-
- IntegratorImageHarmonicMD - Class in etomica.freeenergy.npath
-
Created by andrew on 4/30/17.
- IntegratorImageHarmonicMD(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- IntegratorImageMultistepMD - Class in etomica.freeenergy.npath
-
This integrator implements velocity Verlet algorithm and Tuckerman's
multi-step time step algorithm to handle propagating the spring forces.
- IntegratorImageMultistepMD(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.freeenergy.npath.IntegratorImageMultistepMD
-
- integratorInitialized(IntegratorEvent) - Method in class etomica.data.DataPumpListener
-
- integratorInitialized(IntegratorEvent) - Method in class etomica.data.DataPumpListenerPow
-
- integratorInitialized(IntegratorEvent) - Method in class etomica.data.DataPumpListenerPowStrict
-
- integratorInitialized(IntegratorEvent) - Method in interface etomica.integrator.IntegratorListener
-
Invoked when integration begins.
- integratorInitialized(IntegratorEvent) - Method in class etomica.integrator.IntegratorListenerAction
-
- integratorInitialized(IntegratorEvent) - Method in class etomica.integrator.IntegratorListenerGroupSeries
-
- integratorInitialized(IntegratorEvent) - Method in class etomica.interfacial.FixedWall
-
- integratorInitialized(IntegratorEvent) - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- integratorInitialized(IntegratorEvent) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- integratorInitialized(IntegratorEvent) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- integratorInitialized(IntegratorEvent) - Method in class etomica.nbr.list.NeighborListManager
-
- IntegratorJT - Class in etomica.modules.joulethomson
-
- IntegratorJT(IRandom, IntegratorBox, IntegratorBox) - Constructor for class etomica.modules.joulethomson.IntegratorJT
-
- IntegratorJT.EnsembleToggler - Class in etomica.modules.joulethomson
-
- IntegratorKMC - Class in etomica.kmc
-
- IntegratorKMC(Simulation, PotentialMaster, double, IRandom, ISpecies[], Space) - Constructor for class etomica.kmc.IntegratorKMC
-
- integratorKMC - Variable in class etomica.kmc.SimKMCLJadatom
-
- integratorKMC() - Method in class etomica.kmc.SimKMCLJadatom
-
- integratorKMC - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- integratorKMC() - Method in class etomica.kmc.SimKMCMEAMadatom
-
- IntegratorKMCCluster - Class in etomica.kmc
-
- IntegratorKMCCluster(Simulation, PotentialMaster, double, int, IRandom, ISpecies[], Space) - Constructor for class etomica.kmc.IntegratorKMCCluster
-
- integratorKMCCluster - Variable in class etomica.kmc.SimKMCLJadatom
-
- integratorKMCCluster(double, int, int) - Method in class etomica.kmc.SimKMCLJadatom
-
- integratorKMCCluster - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- integratorKMCCluster(double, int, int) - Method in class etomica.kmc.SimKMCMEAMadatom
-
- integratorLiquid - Variable in class etomica.modules.vle.VLESim
-
- IntegratorListener - Interface in etomica.integrator
-
- IntegratorListenerAction - Class in etomica.integrator
-
An IntegratorListener that performs an action after every integrator step,
optionally with a given interval of integrator steps.
- IntegratorListenerAction(IAction) - Constructor for class etomica.integrator.IntegratorListenerAction
-
- IntegratorListenerAction(IAction, int) - Constructor for class etomica.integrator.IntegratorListenerAction
-
- IntegratorListenerGroupSeries - Class in etomica.integrator
-
A composition of IntegratorListeners that must be performed together and in sequence.
- IntegratorListenerGroupSeries() - Constructor for class etomica.integrator.IntegratorListenerGroupSeries
-
- IntegratorListenerGroupSeries(IntegratorListener[]) - Constructor for class etomica.integrator.IntegratorListenerGroupSeries
-
- IntegratorListenerMD - Interface in etomica.integrator
-
- IntegratorManagerMC - Class in etomica.integrator
-
Integrator manages other Integrators which either act on a Box, or manage
still other Integrators.
- IntegratorManagerMC(IRandom) - Constructor for class etomica.integrator.IntegratorManagerMC
-
- integratorMAP - Variable in class etomica.dimer.EnergyMap
-
- IntegratorMC - Class in etomica.integrator
-
Integrator to perform Metropolis Monte Carlo sampling.
- IntegratorMC(Simulation, PotentialMaster) - Constructor for class etomica.integrator.IntegratorMC
-
- IntegratorMC(PotentialMaster, IRandom, double) - Constructor for class etomica.integrator.IntegratorMC
-
- integratorMC - Variable in class etomica.integrator.IntegratorMD
-
- integratorMC - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- integratorMC - Variable in class etomica.liquidLJ.LjMd3D
-
- integratorMC - Variable in class etomica.modules.adsorption.Adsorption
-
- integratorMC - Variable in class etomica.modules.adsorption.IntegratorHybrid
-
- integratorMC - Variable in class etomica.normalmode.SimHSMDVacancy
-
- integratorMD - Variable in class etomica.dimer.SimDimerLJadatom
-
- integratorMD - Variable in class etomica.dimer.SimDimerLJgb
-
- integratorMD - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- integratorMD - Variable in class etomica.dimer.SimDimerMEAMGB
-
- IntegratorMD - Class in etomica.integrator
-
Superclass of all molecular-dynamics integrators.
- IntegratorMD(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.integrator.IntegratorMD
-
Constructs integrator with a default for non-isothermal sampling.
- integratorMD - Variable in class etomica.modules.adsorption.Adsorption
-
- integratorMD - Variable in class etomica.modules.adsorption.IntegratorHybrid
-
- IntegratorMD.ThermostatType - Enum in etomica.integrator
-
- IntegratorMD.VectorSource - Class in etomica.integrator
-
An AgentSource that permits another vector to be associated with each atom.
- IntegratorMDHarmonicMC - Class in etomica.freeenergy.npath
-
Created by andrew on 4/30/17.
- IntegratorMDHarmonicMC(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- integratorOS - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- integratorOS - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceUa2
-
- integratorOS - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- integratorOS - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- integratorOS - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- integratorOS - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- integratorOverlap - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- integratorOverlap - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- integratorOverlap - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- integratorOverlap - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- integratorOverlap - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- integratorOverlap - Variable in class etomica.normalmode.SimOverlap
-
- integratorOverlap - Variable in class etomica.normalmode.SimOverlapLJ
-
- integratorOverlap - Variable in class etomica.normalmode.SimOverlapLJModule
-
- integratorOverlap - Variable in class etomica.normalmode.SimOverlapModule
-
- integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- integratorOverlap - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- integratorOverlap - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- IntegratorOverlap - Class in etomica.overlap
-
This integrator class manages (2) sub-integrators for an overlap
sampling simulation.
- IntegratorOverlap(Integrator[]) - Constructor for class etomica.overlap.IntegratorOverlap
-
- IntegratorOverlap - Class in etomica.virial.overlap
-
This integrator class manages (2) sub-integrators for an overlap
sampling simulation.
- IntegratorOverlap(Integrator[]) - Constructor for class etomica.virial.overlap.IntegratorOverlap
-
- IntegratorOverlap.ReferenceFracSource - Interface in etomica.overlap
-
- IntegratorPolymer - Class in etomica.modules.rheology
-
Integrator for Brownian dynamics of a polymer in a flow field.
- IntegratorPolymer(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.modules.rheology.IntegratorPolymer
-
- IntegratorPT - Class in etomica.integrator
-
Parallel-tempering integrator.
- IntegratorPT(IRandom, Space) - Constructor for class etomica.integrator.IntegratorPT
-
- IntegratorPT(IRandom, IntegratorPT.MCMoveSwapFactory, Space) - Constructor for class etomica.integrator.IntegratorPT
-
- IntegratorPT.BoxTracker - Class in etomica.integrator
-
Meter that tracks the swapping of the boxes in parallel-tempering
simulation.
- IntegratorPT.MCMoveSwap - Interface in etomica.integrator
-
Interface for a move that swaps two boxes.
- IntegratorPT.MCMoveSwapFactory - Interface in etomica.integrator
-
Interface for a class that can make a MCMove that will swap
the configurations of two boxes.
- IntegratorReset - Class in etomica.action
-
Action that calls the reset method of an integrator.
- IntegratorReset() - Constructor for class etomica.action.IntegratorReset
-
- IntegratorReset(Integrator, boolean) - Constructor for class etomica.action.IntegratorReset
-
- IntegratorRigidIterative - Class in etomica.integrator
-
- IntegratorRigidIterative(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.IntegratorRigidIterative
-
- IntegratorRigidIterative(Simulation, PotentialMaster, double, double, Space) - Constructor for class etomica.integrator.IntegratorRigidIterative
-
- IntegratorRigidIterative.MoleculeAgent - Class in etomica.integrator
-
- IntegratorRigidMatrixIterative - Class in etomica.integrator
-
Integrator implementation of Omelyan's leapfrog integrator for rotational
motion.
- IntegratorRigidMatrixIterative(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative
-
- IntegratorRigidMatrixIterative(Simulation, PotentialMaster, double, double, Space) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative
-
- IntegratorRigidMatrixIterative.AtomAgent - Class in etomica.integrator
-
- IntegratorRigidMatrixIterative.BoxImposePbcMolecule - Class in etomica.integrator
-
- IntegratorRigidMatrixIterative.MoleculeAgent - Class in etomica.integrator
-
- integrators - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- integrators - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- integrators - Variable in class etomica.integrator.IntegratorManagerMC
-
- integrators - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- integrators - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- integrators - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- integrators - Variable in class etomica.normalmode.SimOverlap
-
- integrators - Variable in class etomica.normalmode.SimOverlapLJ
-
- integrators - Variable in class etomica.normalmode.SimOverlapLJModule
-
- integrators - Variable in class etomica.normalmode.SimOverlapModule
-
- integrators - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- integrators - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- integrators - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- integrators - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- integrators - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- integrators - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- integrators - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- integrators - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- integrators - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- integrators - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- integratorSim - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- integratorSim - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- integratorSim - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- IntegratorSmoother(AkimaSplineSmoother) - Constructor for class etomica.math.numerical.AkimaSplineSmootherApp.IntegratorSmoother
-
- IntegratorSmoother(AkimaSplineSmoother) - Constructor for class etomica.math.numerical.AkimaSplineSmootherDyApp.IntegratorSmoother
-
- integratorStep() - Method in class etomica.simulation.BenchSimDCVGCMD
-
- integratorStep() - Method in class etomica.simulation.BenchSimHSMD3D
-
- integratorStep() - Method in class etomica.simulation.BenchSimLJGCMC3D
-
- integratorStep() - Method in class etomica.simulation.BenchSimLJMC3D
-
- integratorStep() - Method in class etomica.simulation.BenchSimSurfacetensionLJMC
-
- integratorStep() - Method in class etomica.simulation.BenchSimSWChain
-
- integratorStepFinished(IntegratorEvent) - Method in class etomica.data.DataPumpListener
-
- integratorStepFinished(IntegratorEvent) - Method in class etomica.data.DataPumpListenerPow
-
- integratorStepFinished(IntegratorEvent) - Method in class etomica.data.DataPumpListenerPowStrict
-
- integratorStepFinished(IntegratorEvent) - Method in interface etomica.integrator.IntegratorListener
-
Invoked at the end of each integrator step.
- integratorStepFinished(IntegratorEvent) - Method in class etomica.integrator.IntegratorListenerAction
-
- integratorStepFinished(IntegratorEvent) - Method in class etomica.integrator.IntegratorListenerGroupSeries
-
- integratorStepFinished(IntegratorEvent) - Method in class etomica.interfacial.FixedWall
-
- integratorStepFinished(IntegratorEvent) - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- integratorStepFinished(IntegratorEvent) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- integratorStepFinished(IntegratorEvent) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- integratorStepFinished(IntegratorEvent) - Method in class etomica.nbr.list.NeighborListManager
-
- integratorStepStarted(IntegratorEvent) - Method in class etomica.data.DataPumpListener
-
- integratorStepStarted(IntegratorEvent) - Method in class etomica.data.DataPumpListenerPow
-
- integratorStepStarted(IntegratorEvent) - Method in class etomica.data.DataPumpListenerPowStrict
-
- integratorStepStarted(IntegratorEvent) - Method in interface etomica.integrator.IntegratorListener
-
Invoked at the beginning of each integrator step.
- integratorStepStarted(IntegratorEvent) - Method in class etomica.integrator.IntegratorListenerAction
-
- integratorStepStarted(IntegratorEvent) - Method in class etomica.integrator.IntegratorListenerGroupSeries
-
- integratorStepStarted(IntegratorEvent) - Method in class etomica.interfacial.FixedWall
-
- integratorStepStarted(IntegratorEvent) - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- integratorStepStarted(IntegratorEvent) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- integratorStepStarted(IntegratorEvent) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- integratorStepStarted(IntegratorEvent) - Method in class etomica.nbr.list.NeighborListManager
-
- integratorTarg - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
-
- integratorTarget - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- integratorTarget - Variable in class etomica.normalmode.SimOverlap
-
- IntegratorThermodynamic - Class in etomica.thermointegration
-
Abstract class suitable as a parent class for thermodynamic integration
integrators.
- IntegratorThermodynamic(Integrator) - Constructor for class etomica.thermointegration.IntegratorThermodynamic
-
Constructs a thermodynamic integrator that operates with the given
sub integrator, which is responsible for exploring configruations at any
given state point.
- IntegratorThermodynamicPEvsT - Class in etomica.thermointegration
-
- IntegratorThermodynamicPEvsT(IntegratorBox) - Constructor for class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- IntegratorTMMC - Class in etomica.tmmc
-
Integrator that implements Transition-Matrix Monte Carlo method.
- IntegratorTMMC(Simulation, PotentialMaster) - Constructor for class etomica.tmmc.IntegratorTMMC
-
- IntegratorTMMC(PotentialMaster, IRandom, double) - Constructor for class etomica.tmmc.IntegratorTMMC
-
- integratorVapor - Variable in class etomica.modules.vle.VLESim
-
- IntegratorVelocityVerlet - Class in etomica.integrator
-
- IntegratorVelocityVerlet(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.IntegratorVelocityVerlet
-
- IntegratorVelocityVerlet(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.integrator.IntegratorVelocityVerlet
-
- IntegratorVelocityVerlet.MyAgent - Class in etomica.integrator
-
- IntegratorVelocityVerletQuaternion - Class in etomica.rotation
-
- IntegratorVelocityVerletQuaternion(Simulation, PotentialMaster, Space) - Constructor for class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- IntegratorVelocityVerletQuaternion(Simulation, PotentialMaster, double, double, Space) - Constructor for class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- IntegratorVelocityVerletQuaternion.AtomAgent - Class in etomica.rotation
-
- IntegratorVelocityVerletQuaternion.MoleculeAgent - Class in etomica.rotation
-
- IntegratorVelocityVerletQuaternion.MyTypeAgent - Class in etomica.rotation
-
- IntegratorVelocityVerletRattle - Class in etomica.integrator
-
Integrator implementing RATTLE algorithm.
- IntegratorVelocityVerletRattle(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.IntegratorVelocityVerletRattle
-
- IntegratorVelocityVerletRattle(Simulation, PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.integrator.IntegratorVelocityVerletRattle
-
- IntegratorVelocityVerletSAM - Class in etomica.modules.sam
-
Special integrator subclass that has the ability to prevent sulfur atoms
from moving in the Y direction.
- IntegratorVelocityVerletSAM(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.modules.sam.IntegratorVelocityVerletSAM
-
- IntegratorVelocityVerletShake - Class in etomica.integrator
-
Integrator implementing SHAKE algorithm.
- IntegratorVelocityVerletShake(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.IntegratorVelocityVerletShake
-
- IntegratorVelocityVerletShake(Simulation, PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.integrator.IntegratorVelocityVerletShake
-
- IntegratorVelocityVerletShake.BondConstraints - Class in etomica.integrator
-
- IntegratorVelocityVerletThreaded - Class in etomica.threaded
-
- IntegratorVelocityVerletThreaded(IRandom, Space, PotentialMaster, int) - Constructor for class etomica.threaded.IntegratorVelocityVerletThreaded
-
- IntegratorVelocityVerletThreaded(PotentialMaster, IRandom, double, double, int, Space) - Constructor for class etomica.threaded.IntegratorVelocityVerletThreaded
-
- IntegratorVerlet - Class in etomica.integrator
-
- IntegratorVerlet(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.IntegratorVerlet
-
- IntegratorVerlet(PotentialMaster, IRandom, double, double, Space) - Constructor for class etomica.integrator.IntegratorVerlet
-
- IntegratorVerlet.Agent - Class in etomica.integrator
-
- intenseFraction - Static variable in class org.jmol.util.Shader
-
- interactionAgentManager - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- interactionAgentManager - Variable in class etomica.modules.catalysis.MeterDensityCO
-
- interactionAgentManager - Variable in class etomica.modules.catalysis.MeterDensityCO2
-
- interactionAgentManager - Variable in class etomica.modules.catalysis.MeterDensityO2
-
- interactionRange - Variable in class etomica.nbr.CriterionSimple
-
- interactionRange - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- interactionTracker - Variable in class etomica.modules.catalysis.Catalysis
-
- InteractionTracker - Class in etomica.modules.catalysis
-
- InteractionTracker(Box, ISpecies) - Constructor for class etomica.modules.catalysis.InteractionTracker
-
- InteractionTracker.CatalysisAgent - Class in etomica.modules.catalysis
-
- InterfacialSW - Class in etomica.modules.interfacial
-
Simulation for interfacial tension module.
- InterfacialSW(Space) - Constructor for class etomica.modules.interfacial.InterfacialSW
-
- InterfacialSWGraphic - Class in etomica.modules.interfacial
-
Graphic UI for interfacial tension module.
- InterfacialSWGraphic(InterfacialSW, Space) - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic
-
- InterfacialSWGraphic.Applet - Class in etomica.modules.interfacial
-
- InterfacialSWGraphic.DataProcessorTensorSplitter - Class in etomica.modules.interfacial
-
Inner class to find the total pressure of the system from the pressure
tensor.
- InterfacialSWGraphic.ModifierBoxSize - Class in etomica.modules.interfacial
-
- interiorColor - Variable in class etomica.modules.droplet.ColorSchemeDropletSurface
-
- intermolecular - Static variable in class org.jmol.script.Token
-
- internalDataSink - Variable in class etomica.data.DataTableWriter
-
- interpolatedDy - Variable in class etomica.math.numerical.AkimaSpline
-
- interpolatedY - Variable in class etomica.math.numerical.AkimaSpline
-
- interPotential - Variable in class etomica.parser.ParserLAMMPS.Stuff
-
- Interpreter - Class in etomica.graph.engine
-
- Interpreter(ConsoleContainer, Environment, Parser) - Constructor for class etomica.graph.engine.Interpreter
-
- Interpreter.InterpreterException - Exception in etomica.graph.engine
-
- InterpreterException(String) - Constructor for exception etomica.graph.engine.Interpreter.InterpreterException
-
- InterpreterException(String, Throwable) - Constructor for exception etomica.graph.engine.Interpreter.InterpreterException
-
- intersectPlane(Point4f, float, int) - Method in class org.jmol.util.BoxInfo
-
returns a set of points defining the geometric object within the given
plane that spans the unit cell within the given margins
- intersectPlane(Point4f, List<Object>, int) - Static method in class org.jmol.util.TriangleData
-
a generic cell - plane intersector -- used for finding the plane through a
unit cell
- intersects(BitSet) - Method in class org.jmol.util.BitSet
-
Returns true if the specified BitSet has any bits set to true that are also set to true in this BitSet.
- interType - Variable in class etomica.potential.Potential0Lrc
-
- interval - Variable in class etomica.data.DataPumpListener
-
- interval - Variable in class etomica.data.DataPumpListenerPow
-
- interval - Variable in class etomica.data.DataPumpListenerPowStrict
-
- interval - Variable in class etomica.data.history.HistoryCollapsing
-
- interval - Variable in class etomica.integrator.Integrator
-
- intervalCount - Variable in class etomica.data.DataPumpListener
-
- intervalCount - Variable in class etomica.data.DataPumpListenerPowStrict
-
- intervalCount - Variable in class etomica.data.history.HistoryCollapsing
-
- intervals - Variable in class etomica.data.DataPumpListenerPow
-
- intoTruncatedOctahedron - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
-
- intparam - Static variable in class org.jmol.script.Token
-
- IntParameters - Class in etomica.graph.operations
-
- IntParameters(byte) - Constructor for class etomica.graph.operations.IntParameters
-
- intproperty - Static variable in class org.jmol.script.Token
-
- intraAgentManager - Variable in class etomica.nbr.PotentialMasterNbr
-
- intramolecular - Static variable in class org.jmol.script.Token
-
- intraPotential - Variable in class etomica.parser.ParserLAMMPS.Stuff
-
- introspect(Object, String, BeanInfo) - Static method in class etomica.units.dimensions.Dimension
-
Method to determine the dimension of a property via introspection.
- IntSet - Class in etomica.virial
-
An IntSet holds an array of integers and can act as a has key.
- IntSet(int[]) - Constructor for class etomica.virial.IntSet
-
- IntSet.PropertyBin - Interface in etomica.virial
-
- intToken(int) - Static method in class org.jmol.script.Token
-
- intValue - Variable in class org.jmol.script.Token
-
- inv() - Method in class org.jmol.util.Quaternion
-
- invalidatePolygons() - Method in class org.jmol.util.MeshSurface
-
- inverse(double) - Method in class etomica.math.function.Function.Exp
-
- inverse(double) - Method in class etomica.math.function.Function.Identity
-
- inverse(double) - Method in class etomica.math.function.Function.Linear
-
- inverse(double) - Method in class etomica.math.function.Function.Log
-
- inverse(double) - Method in class etomica.math.function.Function.Reciprocal
-
- inverse(double) - Method in class etomica.math.function.Function.Sqrt
-
- inverse(double) - Method in class etomica.math.function.FunctionChain
-
Inverts function by calling inverse methods of subfunctions, in reverse order of their addition.
- inverse(double) - Method in interface etomica.math.function.FunctionInvertible
-
- inverse() - Method in class etomica.math.Quaternion
-
Returns the inverse of the Quaternion q given by q^-1 = 1/(norm^2) * q*
- inverse(double) - Method in class etomica.modules.statistics.StatisticsMCGraphic.MyFunctionInvertible
-
- inverse(double) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
-
- inverseProduct3D(Vector, Vector, Vector) - Method in class etomica.potential.P2SpheroPolyhedron
-
- inverseProduct4D(Vector, Vector, Vector) - Method in class etomica.potential.P2SpheroPolyhedron
-
- invert() - Method in class etomica.lattice.LatticePlane
-
Changes the direction of the normal vector so that it points
toward the other side of the plane from its present orientation.
- invert() - Method in class etomica.math.geometry.Plane
-
Changes the direction of the normal vector so that it points
toward the other side of the plane from its present orientation.
- invert() - Method in class etomica.math.numerical.FastFourierTransform
-
Reverse Transformation of discrete data sets
- invert() - Method in interface etomica.space.Tensor
-
Replaces this tensor with its inverse.
- invert() - Method in class etomica.space1d.Tensor1D
-
- invert() - Method in class etomica.space2d.Tensor2D
-
- invert() - Method in class etomica.space3d.RotationTensor3D
-
- invert() - Method in class etomica.space3d.Tensor3D
-
- invert() - Method in class etomica.spaceNd.TensorND
-
- invert() - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to its inverse.
- invert() - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to its inverse.
- invertInPlace(BitSet, int) - Static method in class org.jmol.util.BitSetUtil
-
inverts the bitset bits 0 through n-1,
and returns a reference to the modified bitset
- invertM(Matrix3f) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to the matrix inverse of the passed matrix
m1.
- invertM(Matrix4f) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to the matrix inverse of the passed matrix
m1.
- invertRound(BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Build the inverse and maintain the approximate accuracy.
- invokeAdder(Object) - Method in class etomica.meta.properties.ArrayProperty
-
- invokeAdder(Object) - Method in class etomica.meta.properties.AtomListProperty
-
- invokeAdder(Object) - Method in class etomica.meta.properties.InstanceProperty
-
- invokeAdder(Object) - Method in class etomica.meta.properties.MoleculeListProperty
-
- invokeAdder(Object) - Method in interface etomica.meta.properties.Property
-
- invokeAdder(Object) - Method in class etomica.meta.properties.VectorProperty
-
- invokeCount() - Method in class etomica.meta.properties.ArrayProperty
-
- invokeCount() - Method in class etomica.meta.properties.AtomListProperty
-
- invokeCount() - Method in class etomica.meta.properties.InstanceProperty
-
- invokeCount() - Method in class etomica.meta.properties.MoleculeListProperty
-
- invokeCount() - Method in interface etomica.meta.properties.Property
-
- invokeCount() - Method in class etomica.meta.properties.VectorProperty
-
- invokeReader() - Method in class etomica.meta.properties.ArrayProperty
-
- invokeReader(int) - Method in class etomica.meta.properties.ArrayProperty
-
- invokeReader() - Method in class etomica.meta.properties.AtomListProperty
-
- invokeReader(int) - Method in class etomica.meta.properties.AtomListProperty
-
- invokeReader() - Method in class etomica.meta.properties.InstanceProperty
-
- invokeReader(int) - Method in class etomica.meta.properties.InstanceProperty
-
- invokeReader() - Method in class etomica.meta.properties.MoleculeListProperty
-
- invokeReader(int) - Method in class etomica.meta.properties.MoleculeListProperty
-
- invokeReader() - Method in interface etomica.meta.properties.Property
-
- invokeReader(int) - Method in interface etomica.meta.properties.Property
-
- invokeReader() - Method in class etomica.meta.properties.VectorProperty
-
- invokeReader(int) - Method in class etomica.meta.properties.VectorProperty
-
- invokeRemover(Object) - Method in class etomica.meta.properties.ArrayProperty
-
- invokeRemover(Object) - Method in class etomica.meta.properties.AtomListProperty
-
- invokeRemover(Object) - Method in class etomica.meta.properties.InstanceProperty
-
- invokeRemover(Object) - Method in class etomica.meta.properties.MoleculeListProperty
-
- invokeRemover(Object) - Method in interface etomica.meta.properties.Property
-
- invokeRemover(Object) - Method in class etomica.meta.properties.VectorProperty
-
- invokeWriter(Object...) - Method in class etomica.meta.properties.ArrayProperty
-
- invokeWriter(int, Object...) - Method in class etomica.meta.properties.ArrayProperty
-
- invokeWriter(Object...) - Method in class etomica.meta.properties.AtomListProperty
-
- invokeWriter(int, Object...) - Method in class etomica.meta.properties.AtomListProperty
-
- invokeWriter(Object...) - Method in class etomica.meta.properties.InstanceProperty
-
- invokeWriter(int, Object...) - Method in class etomica.meta.properties.InstanceProperty
-
- invokeWriter(Object...) - Method in class etomica.meta.properties.MoleculeListProperty
-
- invokeWriter(int, Object...) - Method in class etomica.meta.properties.MoleculeListProperty
-
- invokeWriter(Object...) - Method in interface etomica.meta.properties.Property
-
- invokeWriter(int, Object...) - Method in interface etomica.meta.properties.Property
-
- invokeWriter(Object...) - Method in class etomica.meta.properties.VectorProperty
-
- invokeWriter(int, Object...) - Method in class etomica.meta.properties.VectorProperty
-
- ionic - Static variable in class org.jmol.script.Token
-
- iopt - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- iOrientation - Variable in class etomica.atom.AtomOriented
-
- iOrientation - Variable in class etomica.atom.AtomOrientedDynamic
-
- IOrientation - Interface in etomica.space
-
Interface for a class that specifies an orientation in space.
- IOrientation2D - Interface in etomica.space2d
-
Interface for a class that specifies an orientation in a 2D space.
- IOrientation3D - Interface in etomica.space3d
-
Interface for an orientation in 3D.
- IOrientationFull3D - Interface in etomica.space3d
-
Interface representing an orientation in 3D.
- iparams - Static variable in class etomica.models.co2.P2CO2H2OWheatley
-
- iPosition - Variable in class etomica.virial.CoordinatePairMoleculeSet
-
- IPotential - Interface in etomica.potential
-
- IPotential0Lrc - Interface in etomica.potential
-
Interface for a long-range correction potential.
- IPotential0MoleculeLrc - Interface in etomica.potential
-
Interface for a long-range correction potential.
- IPotentialAtomic - Interface in etomica.potential
-
- IPotentialAtomicMultibody - Interface in etomica.potential
-
Interface for an atomic non-additive potential.
- IPotentialCalculationThreaded - Interface in etomica.threaded
-
- IPotentialCalculationWallForce - Interface in etomica.modules.rosmosis
-
- IPotentialMolecular - Interface in etomica.potential
-
- IPotentialMolecularSecondDerivative - Interface in etomica.potential
-
- IPotentialMolecularTorque - Interface in etomica.potential
-
- IPotentialTorque - Interface in etomica.potential
-
- iPotParts - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- ipr - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- iRand - Variable in class etomica.normalmode.MCMoveHarmonic
-
- IRandom - Interface in etomica.util.random
-
Interface for random number generation.
- Iron - Class in etomica.chem.elements
-
Class for the Iron element.
- Iron(String) - Constructor for class etomica.chem.elements.Iron
-
- Iron(String, double) - Constructor for class etomica.chem.elements.Iron
-
- iroots() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Generate the integer roots of the polynomial.
- irpowex - Static variable in class etomica.potential.P2HydrogenPatkowski
-
- irpowex - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- irpowsp - Static variable in class etomica.potential.P2HydrogenPatkowski
-
- irpowsp - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- is864 - Variable in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- is864() - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- IS_EMPTY - Static variable in class etomica.compatibility.Feature
-
- IS_EQUAL - Static variable in class etomica.compatibility.Feature
-
- isAB(Object) - Static method in class org.jmol.util.Escape
-
- isAccepted() - Method in class etomica.integrator.mcmove.MCMoveTrialCompletedEvent
-
- isActive - Variable in class etomica.action.Activity
-
- isActive() - Method in class etomica.action.Activity
-
Indicates if the integrator has been started and has not yet completed.
- isActive() - Method in class etomica.data.DataAccumulator
-
- isActiveLevel(int) - Static method in class org.jmol.util.Logger
-
Tells if a logging level is active.
- isAD(Object) - Static method in class org.jmol.util.Escape
-
- isAdiabatic() - Method in class etomica.graphics.DeviceThermoSlider
-
- isAdiabatic() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- isAdjustStepFraction() - Method in class etomica.overlap.IntegratorOverlap
-
Sets whether to adjust the number of relative number of steps for each
sub-integrator.
- isAdjustStepFreq() - Method in class etomica.virial.overlap.IntegratorOverlap
-
Sets whether to adjust the number of relative number of steps for each
sub-integrator.
- isAF(Object) - Static method in class org.jmol.util.Escape
-
- isAFF(Object) - Static method in class org.jmol.util.Escape
-
- isAFFF(Object) - Static method in class org.jmol.util.Escape
-
- isAFloat(Object) - Static method in class org.jmol.util.Escape
-
- isAI(Object) - Static method in class org.jmol.util.Escape
-
- isAII(Object) - Static method in class org.jmol.util.Escape
-
- isAllEVal() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
- isAllowEqualElements() - Method in class etomica.lattice.IndexIteratorTriangular
-
- isAllWV() - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
- isAlpha - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- isAlpha - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- isAntialiased() - Method in class org.jmol.util.GData
-
is full scene / oversampling antialiasing in effect
- isAP(Object) - Static method in class org.jmol.util.Escape
-
- isAppend() - Method in class etomica.action.XYZWriter
-
- isAppending() - Method in class etomica.data.DataLogger
-
- isApplyToMolecules() - Method in class etomica.action.BoxImposePbc
-
Returns the value of applyToMolecules.
- isaromatic - Static variable in class org.jmol.script.Token
-
- isArticulated(Graph, int, int) - Method in class etomica.graph.property.FactorFFT
-
- IsArticulationPair - Class in etomica.graph.property
-
- IsArticulationPair() - Constructor for class etomica.graph.property.IsArticulationPair
-
- isArticulationPair(Graph, int, int) - Method in class etomica.graph.property.IsArticulationPair
-
- isArticulationPair(int, int) - Method in class etomica.virial.cluster.ClusterGenerator
-
determines if the given pair of points is an articulation pair.
- IsArticulationPoint - Class in etomica.graph.property
-
- IsArticulationPoint() - Constructor for class etomica.graph.property.IsArticulationPoint
-
- isArticulationPoint(Graph, int) - Method in class etomica.graph.property.IsArticulationPoint
-
- isArticulationPoint(int) - Method in class etomica.virial.cluster.ClusterGenerator
-
Determines if the given point is an articulation point.
- isAS(Object) - Static method in class org.jmol.util.Escape
-
- isASS(Object) - Static method in class org.jmol.util.Escape
-
- isAssociated(IAtom, IAtom) - Method in interface etomica.association.AssociationDefinition
-
- isAssociated(IMolecule, IMolecule) - Method in interface etomica.association.AssociationDefinitionMolecule
-
- isAssociated(IAtom, IAtom) - Method in class etomica.association.BiasVolume
-
- isAssociated(IMolecule, IMolecule) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
Function to check for bonding
calculate the distance between atom1 and atom2
- isAssociated(IMolecule, IMolecule) - Method in class etomica.association.BiasVolumeAceticAcid
-
Function to check for bonding
calculate the distance between atom1 and atom2
- isAssociated(IAtom, IAtom) - Method in class etomica.association.BiasVolumeCube
-
Function to check for bonding
- isAssociated(IMolecule, IMolecule) - Method in class etomica.association.BiasVolumeMolecule
-
- isAssociated(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphere
-
Function to check for bonding
calculate the distance between atom1 and atom2
- isAssociated(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphereOriented
-
Function to check for bonding
calculate the distance between atom1 and atom2
- isAssociated(IAtom, IAtom) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
Function to check for bonding
calculate the distance between atom1 and atom2
- isAssociation - Variable in class etomica.models.OPLS.P2AceticAcidTwoSite
-
- isAssociation - Variable in class etomica.models.water.P2HardAssociationGCPMReference
-
- isAssociation - Variable in class etomica.models.water.PNWaterGCPMThreeSite
-
- isAV(Object) - Static method in class org.jmol.util.Escape
-
- isAxisSymmetric - Variable in class etomica.species.SpeciesSpheresRotating
-
- isAxisSymmetric() - Method in class etomica.species.SpeciesSpheresRotating
-
- isB - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- isBeta - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- isBeta - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- isBeta - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- isBetaHCP - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- isBetaHCP - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- isBetaHCP - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- isBetaLatticeSum - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- isBetaPhase - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- isBetaPhase() - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- isBi - Variable in class etomica.graph.model.comparators.ComparatorBiConnected
-
- isBi - Variable in class etomica.graph.operations.ReeHoover
-
- isBi - Variable in class etomica.graph.property.FFTDecomposition
-
- isBiColor() - Method in enum org.jmol.constant.EnumStereoMode
-
- IsBiconnected - Class in etomica.graph.property
-
- IsBiconnected() - Constructor for class etomica.graph.property.IsBiconnected
-
- isBigInteger() - Method in class etomica.veos.bigdecimal.BigSurd
-
True if the value is integer.
- isBigInteger() - Method in class etomica.veos.bigdecimal.Rational
-
True if the value is integer.
- isBonded() - Method in class etomica.nbr.CriterionBondedSimple
-
- isBonded(IAtom, IAtom) - Method in class etomica.potential.P2HardBondedList
-
Returns true if the pair of atoms are on each others' bonded list; false otherwise.
- isBonded(IAtomList) - Method in class etomica.potential.P2HardBondedList
-
- isBoundaryWall() - Method in class etomica.nbr.CriterionPositionWall
-
Returns true if the walls are at the box boundaries.
- isBroken - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- isCartesianExport() - Method in class org.jmol.g3d.Graphics3D
-
- isCellEditable(int, int) - Method in class etomica.graphics.DeviceTableModelGeneric
-
- isCellEditable(int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- isCellEditable(int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- isCellEditable(int, int) - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- isClipped(int, int) - Method in class org.jmol.util.GData
-
- isClipped3(int, int, int) - Method in class org.jmol.util.GData
-
- isClippedXY(int, int, int) - Method in class org.jmol.util.GData
-
- isClippedZ(int) - Method in class org.jmol.util.GData
-
- isCloseFileEachTime() - Method in class etomica.data.DataLogger
-
- isCO2 - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
-
- isColixColorInherited(short) - Static method in class org.jmol.util.Colix
-
- isColixLastAvailable(short) - Static method in class org.jmol.util.Colix
-
- isColixTranslucent(short) - Static method in class org.jmol.util.Colix
-
- isCollapseOnReset() - Method in class etomica.data.history.HistoryComplete
-
Returns true if the history is collapsed (to 100 data points) when reset
is called.
- isColorSolid - Variable in class org.jmol.util.MeshSurface
-
- isCompatible(Edge) - Method in interface etomica.graph.model.Edge
-
- isCompatible(Edge) - Method in class etomica.graph.model.impl.EdgeImpl
-
- isCompatible(Metadata) - Method in class etomica.graph.model.impl.MetadataImpl
-
- isCompatible(Node) - Method in class etomica.graph.model.impl.NodeImpl
-
- isCompatible(Metadata) - Method in interface etomica.graph.model.Metadata
-
- isCompatible(Node) - Method in interface etomica.graph.model.Node
-
- isCon - Variable in class etomica.graph.operations.SplitGraph
-
- isConnected - Variable in class etomica.graph.property.HasSimpleArticulationPoint
-
- isConnected() - Method in class etomica.graph.property.HasSimpleArticulationPoint
-
- IsConnected - Class in etomica.graph.property
-
- IsConnected() - Constructor for class etomica.graph.property.IsConnected
-
- isConnected(int) - Method in class etomica.virial.cluster.ClusterGenerator
-
Determines if the cluster is connected after removal of the
given node.
- isConnected() - Method in class etomica.virial.cluster.ClusterGenerator
-
Determines if the cluster is connected.
- isContextClass(Class) - Static method in class etomica.server.core.construction.Construction
-
- isDead() - Method in interface etomica.graph.isomorphism.SearchState
-
- isDead() - Method in class etomica.graph.isomorphism.UllmanSearchState
-
- isDead() - Method in class etomica.graph.isomorphism.VF2SearchState
-
- isDead() - Method in class etomica.graph.isomorphism.VFSearchState
-
- isDecimalMode() - Method in class etomica.util.ScientificFormat
-
- isDecimalSeparatorAlwaysShown() - Method in class etomica.util.ScientificFormat
-
- isDirectedTowardsCamera(short) - Method in class org.jmol.g3d.Graphics3D
-
- isDirectedTowardsCamera(short) - Method in class org.jmol.util.GData
-
- isDisplayAntialiased() - Method in class org.jmol.util.GData
-
is full scene / oversampling antialiasing GENERALLY in effect
- isDoClear() - Method in class etomica.graphics.DisplayPlot
-
- isDoLatticeSum - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- isDoLegend() - Method in class etomica.graphics.DisplayPlot
-
Accessor for flag determining if a legend is to be shown.
- isDoPBC() - Method in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
-
- isDoPBC() - Method in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
-
- isDoScaling() - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- isDoWiggle() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- isDynamic - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- isDynamic - Variable in class etomica.AlkaneEH.SpeciesMethane
-
- isDynamic - Variable in class etomica.chem.models.Model
-
- isDynamic - Variable in class etomica.models.nitrogen.SpeciesN2
-
- isDynamic - Variable in class etomica.models.nitrogen.SpeciesN2B
-
- isDynamic - Variable in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- isDynamic - Variable in class etomica.models.water.SpeciesWater3P
-
- isDynamic - Variable in class etomica.models.water.SpeciesWater3POriented
-
- isDynamic - Variable in class etomica.models.water.SpeciesWater4P
-
- isDynamic - Variable in class etomica.models.water.SpeciesWater4PCOM
-
- isDynamic - Variable in class etomica.models.water.SpeciesWater4POriented
-
- isDynamic - Variable in class etomica.normalmode.SpeciesHSDimer
-
- isDynamic - Variable in class etomica.paracetamol.SpeciesParacetamol
-
- isDynamic - Variable in class etomica.species.SpeciesSpheres
-
- isDynamic() - Method in class etomica.species.SpeciesSpheres
-
- isDynamic - Variable in class etomica.species.SpeciesSpheresCustom
-
- isDynamic() - Method in class etomica.species.SpeciesSpheresCustom
-
- isDynamic - Variable in class etomica.species.SpeciesSpheresHetero
-
- isDynamic() - Method in class etomica.species.SpeciesSpheresHetero
-
- isDynamic - Variable in class etomica.species.SpeciesSpheresMono
-
- isDynamic() - Method in class etomica.species.SpeciesSpheresMono
-
- isDynamic - Variable in class etomica.virial.Species7SiteRigidSF6
-
- isDynamic - Variable in class etomica.virial.SpeciesAnthracene3site464
-
- isDynamic - Variable in class etomica.virial.SpeciesAnthracene3site545
-
- isDynamic - Variable in class etomica.virial.SpeciesMethane
-
- isDynamic - Variable in class etomica.virial.SpeciesPh3site464
-
- isDynamic - Variable in class etomica.virial.SpeciesPh3site545
-
- isDynamic - Variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- isDynamic - Variable in class etomica.virial.SpeciesTraPPECO2
-
- isDynamic - Variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- isDynamic - Variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- isEditable() - Method in class etomica.graphics.DeviceBox
-
- isElementary() - Method in class etomica.virial.cluster.ClusterGenerator
-
Convenience method to determine whether the cluster is elementary or not.
- isEmpty() - Method in class etomica.atom.AtomArrayList
-
- isEmpty() - Method in class etomica.graph.model.GraphList
-
- isEmpty(Graph) - Method in class etomica.graph.property.FactorFFT
-
- isEmpty(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
- isEmpty() - Method in class etomica.molecule.MoleculeArrayList
-
- isEmpty() - Method in class etomica.util.collections.IndexMap
-
- isEmpty() - Method in class org.jmol.util.BitSet
-
Returns true if this BitSet contains no bits that are set to
true.
- isEnabled() - Method in class etomica.graphics.DeviceSlider
-
- isEnabled(IPotentialAtomic) - Method in class etomica.potential.PotentialGroup
-
Returns true if the potential is in this group and has not been disabled
via a previous call to setEnabled; returns false otherwise.
- isEnabled() - Method in class etomica.potential.PotentialMaster
-
- isEnabled(IPotentialAtomic) - Method in class etomica.potential.PotentialMaster
-
Returns true if the potential is in this group and has not been disabled
via a previous call to setEnabled; returns false otherwise.
- isEnabled(IPotentialMolecular) - Method in class etomica.potential.PotentialMaster
-
Returns true if the potential is in this group and has not been disabled
via a previous call to setEnabled; returns false otherwise.
- isEnabled() - Method in class etomica.potential.PotentialMasterLrc
-
- isEnabled() - Method in class etomica.util.Grabber.ActionCornerSetter
-
- isEnabled - Variable in class etomica.util.Grabber.DefaultMouseListener
-
- isEnablePBC() - Method in class etomica.models.nitrogen.P2Nitrogen
-
- isEqualTo(Quaternion) - Method in class etomica.math.Quaternion
-
Returns whether the Quaternion is equal to another given Quaternion p
- isExpanded - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- isExponentialMode() - Method in class etomica.util.ScientificFormat
-
- isFatal - Variable in exception etomica.graph.view.rasterizer.SVGConverterException
-
Defines whether or not this is a fatal error condition
- isFatal() - Method in exception etomica.graph.view.rasterizer.SVGConverterException
-
- isFeasiblePair(NodePair) - Method in interface etomica.graph.isomorphism.SearchState
-
- isFeasiblePair(NodePair) - Method in class etomica.graph.isomorphism.UllmanSearchState
-
- isFeasiblePair(NodePair) - Method in class etomica.graph.isomorphism.VF2SearchState
-
- isFeasiblePair(NodePair) - Method in class etomica.graph.isomorphism.VFSearchState
-
- IsFFT - Class in etomica.graph.property
-
Property class that determines if a diagram can be decomposed by FFT.
- IsFFT() - Constructor for class etomica.graph.property.IsFFT
-
- IsFFT - Class in etomica.virial
-
- IsFFT() - Constructor for class etomica.virial.IsFFT
-
- isFile(File) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Returns true if f is a File.
- isFitToWindow() - Method in class etomica.graphics.DisplayTable
-
Accessor method for flag determining if table is squeezed to fit in
window.
- isFlexibleMode() - Method in class etomica.util.ScientificFormat
-
- isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- isFoundReverse - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- isGamma - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- isGamma - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- isGoal() - Method in interface etomica.graph.isomorphism.SearchState
-
- isGoal() - Method in class etomica.graph.isomorphism.UllmanSearchState
-
- isGoal() - Method in class etomica.graph.isomorphism.VF2SearchState
-
- isGoal() - Method in class etomica.graph.isomorphism.VFSearchState
-
- isGraphic - Variable in class etomica.AlkaneEH.CH4NVT.Param
-
- isGraphic - Variable in class etomica.AlkaneEH.DHS_NVT.Param
-
- isGraphic - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- isGraphic - Variable in class etomica.dielectric.DHS_NVT.Param
-
- isGraphic - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- isGraphic - Variable in class etomica.dielectric.TIP4P_NVT.Param
-
- isGraphics - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- isGroupingUsed() - Method in class etomica.util.ScientificFormat
-
- isHeadless() - Method in interface org.jmol.api.ApiPlatform
-
- isHeadless() - Method in class org.jmol.awt.Platform
-
- isHetero(String) - Static method in class org.jmol.viewer.JmolConstants
-
- isHOptimizer() - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- isIce - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- isIce - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- isIce - Variable in class etomica.models.water.ConfigurationFileTIP4P
-
- isIgnoreOverlap() - Method in class etomica.action.IntegratorReset
-
- isIgnoreOverlap() - Method in class etomica.action.SimulationRestart
-
- isIgnoreOverlap() - Method in class etomica.zeolite.ZeoliteSimStart
-
- isIllegal() - Method in class etomica.math.Quaternion
-
Returns true if even a single component of the quaternion is either infinite or NaN
- isIncludeAdiabatic() - Method in class etomica.graphics.DeviceThermoSelector
-
- isIncludeLrc() - Method in class etomica.data.meter.MeterHyperVirial
-
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- isIncludeLrc() - Method in class etomica.data.meter.MeterPotentialEnergy
-
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- isIncludeLrc() - Method in class etomica.data.meter.MeterPressure
-
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- isIncludeLrc() - Method in class etomica.data.meter.MeterPressureMolecular
-
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- isIncludeLrc() - Method in class etomica.data.meter.MeterPressureTensor
-
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- isIncludeLrc() - Method in class etomica.liquidLJ.MeterPU
-
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- isIncludeLrc() - Method in class etomica.modules.vle.MeterPressure2
-
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- isIncludeLrc() - Method in class etomica.normalmode.MeterPressureSuperBox
-
Indicates whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- isIncludeLrc() - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- isIncludeLrc() - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- isIncludeLrc() - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- isIncludeLrc() - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- isIncludeLrc() - Method in class etomica.potential.IteratorDirective
-
Sets flag indicating if lrc potentials (long-range correction) should be
included.
- isIndexedProperty() - Method in class etomica.meta.properties.ArrayProperty
-
Gets the value of the property indexedProperty.
- isIndexedProperty() - Method in class etomica.meta.properties.AtomListProperty
-
Gets the value of the property indexedProperty.
- isIndexedProperty() - Method in class etomica.meta.properties.InstanceProperty
-
Gets the value of the property indexedProperty.
- isIndexedProperty() - Method in class etomica.meta.properties.MoleculeListProperty
-
Gets the value of the property indexedProperty.
- isIndexedProperty() - Method in interface etomica.meta.properties.Property
-
Gets the value of the property indexedProperty.
- isIndexedProperty() - Method in class etomica.meta.properties.VectorProperty
-
Gets the value of the property indexedProperty.
- isInDisplayRange(int, int) - Method in class org.jmol.util.GData
-
- isInitialized() - Method in class etomica.integrator.Integrator
-
- isInteger() - Method in class etomica.graphics.DeviceBox
-
- isInteger() - Method in class etomica.veos.bigdecimal.Rational
-
True if the value is integer and in the range of the standard integer.
- isIntegerDisplay() - Method in class etomica.graphics.DisplayTextBox
-
- isIntegerFrac() - Method in class etomica.veos.bigdecimal.Rational
-
True if the value is a fraction of two integers in the range of the standard integer.
- isInteractingList - Variable in class etomica.nbr.list.molecule.MoleculePotentialList
-
- isInteractive - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- isInteractive - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- isInteractive - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- isInteractive - Variable in class etomica.virial.cluster.VirialDiagrams
-
- isInteractive - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- isInteractive - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- isInteractive - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- isInteractive - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- isInteractive - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- isInTetrahedron(Point3f, Point3f, Point3f, Point3f, Point3f, Point4f, Vector3f, Vector3f, Vector3f, boolean) - Static method in class org.jmol.util.Measure
-
- isIntraMolecular() - Method in class etomica.nbr.CriterionMolecular
-
Flag indicating whether to accept intra- (if argument is true) or inter-
(if argument is false) molecular pairs.
- isIsoFree() - Method in class etomica.graph.engine.impl.ConstructorColoredImpl
-
- isIsoFree() - Method in class etomica.graph.engine.impl.ConstructorMonoImpl
-
- isIsoFree() - Method in interface etomica.graph.engine.Parser.ConstructorColored
-
- isIsoFree() - Method in interface etomica.graph.engine.Parser.ConstructorMono
-
- isIsomorphOf(ClusterDiagram) - Method in class etomica.virial.cluster.ClusterDiagram
-
Returns true if this cluster is an isomorph of the given cluster.
- isIsothermal() - Method in class etomica.graphics.DeviceThermoSlider
-
- isIsothermal() - Method in class etomica.integrator.IntegratorBox
-
- isIsothermal() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- iskiosk - Static variable in class org.jmol.script.Token
-
- isLazySafe() - Method in interface g3dsys.control.IndexIterator
-
Indicates whether it is appropriate to simply scale the original
boundary lines when in 'large box' mode.
- isLiquid - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
-
- isLJ - Variable in class etomica.normalmode.MeterSolidProps
-
- isLS - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- isMatch(String, String, boolean, boolean) - Static method in class org.jmol.util.TextFormat
-
- isMaximumScore() - Method in class etomica.virial.cluster.ClusterGenerator
-
Determines if the cluster has a maximum score.
- isMerged - Variable in class org.jmol.util.MeshSurface
-
- ISMORPHS_COUNT - Static variable in class etomica.graph.isomorphism.Match
-
- isMovable() - Method in class etomica.graphics.DisplayCanvas
-
- isMovable() - Method in class etomica.graphics.DisplayPolytope
-
- isNaN() - Method in interface etomica.data.IData
-
Returns true if any data value is true for Double.isNaN
- isNaN() - Method in class etomica.data.types.DataDouble
-
Returns true if the this instance's value is NaN.
- isNaN() - Method in class etomica.data.types.DataDoubleArray
-
Returns true if any element of the encapsulated array is not-a-number, as
given by Double.isNaN.
- isNaN() - Method in class etomica.data.types.DataDoubleBDArray
-
- isNaN() - Method in class etomica.data.types.DataGroup
-
- isNaN() - Method in class etomica.data.types.DataTensor
-
Returns true if any vector element is not-a-number, as given by
Double.isNaN.
- isNaN() - Method in class etomica.data.types.DataVector
-
Returns true if any vector element is not-a-number, as given by Double.isNaN.
- isNaN() - Method in interface etomica.space.Tensor
-
- isNaN() - Method in interface etomica.space.Vector
-
Returns true if any element of the vector is not-a-number.
- isNaN() - Method in class etomica.space1d.Tensor1D
-
- isNaN() - Method in class etomica.space1d.Vector1D
-
- isNaN() - Method in class etomica.space2d.Tensor2D
-
- isNaN() - Method in class etomica.space2d.Vector2D
-
- isNaN() - Method in class etomica.space3d.Tensor3D
-
- isNaN() - Method in class etomica.space3d.Vector3D
-
- isNaN() - Method in class etomica.spaceNd.TensorND
-
- isNaN() - Method in class etomica.spaceNd.VectorND
-
- isNaturalIsotope(String) - Static method in class org.jmol.util.Elements
-
- isNewPair - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- isNewPair - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- isNodalPoint(int) - Method in class etomica.virial.cluster.ClusterGenerator
-
Determines if the given node is a nodal point.
- isNominallyPerParticleFrequency() - Method in class etomica.integrator.mcmove.MCMoveBox
-
Indicates whether this move should nominally be performed at a frequency
proportional to the number of molecules in the box.
- IsoFree - Class in etomica.graph.operations
-
- IsoFree() - Constructor for class etomica.graph.operations.IsoFree
-
- isoFree - Variable in class etomica.graph.operations.Split
-
- IsoFree.IsoFreeParams - Class in etomica.graph.operations
-
- IsoFreeParams() - Constructor for class etomica.graph.operations.IsoFree.IsoFreeParams
-
- IsomorphismFilter - Class in etomica.graph.iterators.filters
-
- IsomorphismFilter(GraphIterator) - Constructor for class etomica.graph.iterators.filters.IsomorphismFilter
-
- IsomorphismFilter(GraphIterator, GlobalFilter.SignatureMaker) - Constructor for class etomica.graph.iterators.filters.IsomorphismFilter
-
- IsomorphismPrefilteredPartitionedIterator - Class in etomica.graph.iterators
-
- IsomorphismPrefilteredPartitionedIterator(Map<Character, Byte>, Map<Character, Byte>) - Constructor for class etomica.graph.iterators.IsomorphismPrefilteredPartitionedIterator
-
- isOneEVal() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
- isOneEVal() - Method in class etomica.normalmode.IntegratorHarmonic
-
- isOneOf(String, String) - Static method in class org.jmol.util.Parser
-
- isOneWV() - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
- isOneWV() - Method in class etomica.normalmode.IntegratorHarmonic
-
- isOnlyHardRod - Variable in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- isosurface - Static variable in class org.jmol.script.Token
-
- isosurfacekey - Static variable in class org.jmol.script.Token
-
- isosurfacepropertysmoothing - Static variable in class org.jmol.script.Token
-
- isosurfacepropertysmoothingpower - Static variable in class org.jmol.script.Token
-
- isothermal - Variable in class etomica.integrator.IntegratorBox
-
- isPaletteVariable(byte) - Static method in enum org.jmol.constant.EnumPalette
-
- isPass2 - Variable in class org.jmol.util.GData
-
- isPass2() - Method in class org.jmol.util.GData
-
- isPauseAfterEachAction() - Method in class etomica.action.activity.ActivityGroupSeries
-
- isPaused() - Method in class etomica.action.activity.ActivityGroupSeries
-
- isPaused() - Method in class etomica.action.Activity
-
Queries whether the integrator is in a state of being paused.
- ISpecies - Interface in etomica.species
-
An ISpecies holds information about how to construct a molecule, and creates molecules on demand.
- ISpeciesOriented - Interface in etomica.species
-
- isPeriodic - Variable in class etomica.lattice.RectangularLatticeNbrIterator
-
- isPositive() - Method in class etomica.veos.BigValue
-
- isPositive() - Method in interface etomica.veos.IBigValue
-
Returns true if this instance has a value greater than zero.
- isPositive() - Method in class etomica.veos.MyBigDecimal
-
- isPositiveSide(Vector) - Method in class etomica.lattice.LatticePlane
-
Returns true if the given point is on the side of the
plane toward which the normal vector points.
- isPositiveSide(Vector) - Method in class etomica.math.geometry.Plane
-
Returns true if the given point is on the side of the
plane or over the side of the plane by epsilon or less
toward which the normal vector points.
- isPotentialSite(String, IMolecularModel_SpeciesFactory) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- IsPotentialSiteMoreThanOne() - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- IsPotentialSiteMoreThanOne() - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- IsPotentialSiteMoreThanOne() - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- IsPotentialSiteMoreThanOne() - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- IsPotentialSiteMoreThanOne() - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- isPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- isPT2 - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- isPT2 - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- isPureQuaternion() - Method in class etomica.math.Quaternion
-
Returns whether the Quaternion is pure or not
- isqrt(int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate floor(sqrt(n)).
- isqrt(long) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate floor(sqrt(n)).
- isqrt(BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate floor(sqrt(n)).
- isQuiet() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- isQuiet() - Method in class etomica.nbr.list.NeighborListManager
-
- isRadical - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
-
- isRadical(IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
This function return true if the given atom is a radical (meaning that
it has only one unreacted site).
- isRational() - Method in class etomica.veos.bigdecimal.BigSurd
-
True if the value is rational.
- isReadable() - Method in class etomica.graph.view.rasterizer.SVGConverterDocumentSource
-
- isReadable() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
-
- isReadable() - Method in interface etomica.graph.view.rasterizer.SVGConverterSource
-
Checks if source can be read
- isReadable() - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
-
- isReference - Variable in class etomica.overlap.MeterOverlap
-
- isRejectable - Variable in class etomica.normalmode.IntegratorHarmonic
-
- isRejectable - Variable in class etomica.normalmode.MCMoveHarmonic
-
- isRejectable() - Method in class etomica.normalmode.MCMoveHarmonic
-
- isRemoveSpeciesAfterAlertFlag() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- isRepeatCurrentAction() - Method in class etomica.action.activity.Controller
-
Returns value of repeatCurrentAction flag.
- isRescalingToFitVolume() - Method in class etomica.config.ConfigurationLattice
-
Returns the resizeLatticeToFitVolume flag.
- isRescalingToFitVolume() - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
Returns the resizeLatticeToFitVolume flag.
- isRescalingToFitVolume() - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
Returns the resizeLatticeToFitVolume flag.
- isResidual() - Method in class etomica.data.meter.MeterWidomInsertion
-
Accessor for flag specifying if full or residual chemical potential is
computed
- isResizable() - Method in class etomica.graphics.DisplayCanvas
-
- isResizable() - Method in class etomica.graphics.DisplayPolytope
-
- isRootPoint(int) - Method in class etomica.virial.cluster.ClusterDiagram
-
returns true if the given point is a root point
- isSameAs(String) - Method in class etomica.graph.view.rasterizer.SVGConverterDocumentSource
-
- isSameAs(String) - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
-
- isSameAs(String) - Method in interface etomica.graph.view.rasterizer.SVGConverterSource
-
Checks if same as source described by srcStr
- isSameAs(String) - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
-
- isSameColor(Edge) - Method in interface etomica.graph.model.Edge
-
- isSameColor(Edge) - Method in class etomica.graph.model.impl.EdgeImpl
-
- isSameColor(Metadata) - Method in class etomica.graph.model.impl.MetadataImpl
-
- isSameColor(Node) - Method in class etomica.graph.model.impl.NodeImpl
-
- isSameColor(Metadata) - Method in interface etomica.graph.model.Metadata
-
- isSameColor(Node) - Method in interface etomica.graph.model.Node
-
- isSameFileEachTime() - Method in class etomica.data.DataLogger
-
- isSameId(Edge) - Method in interface etomica.graph.model.Edge
-
- isSameId(Edge) - Method in class etomica.graph.model.impl.EdgeImpl
-
- isSameId(Node) - Method in class etomica.graph.model.impl.NodeImpl
-
- isSameId(Node) - Method in interface etomica.graph.model.Node
-
- isSameType(Metadata) - Method in class etomica.graph.model.impl.EdgeImpl
-
- isSameType(Metadata) - Method in class etomica.graph.model.impl.MetadataImpl
-
- isSameType(Metadata) - Method in class etomica.graph.model.impl.NodeImpl
-
- isSameType(Metadata) - Method in interface etomica.graph.model.Metadata
-
- isSatisfied(FeatureSet) - Method in class etomica.compatibility.ClassRequirement
-
- isSatisfied(FeatureSet) - Method in class etomica.compatibility.FeatureRequirement
-
- isSatisfied(FeatureSet) - Method in class etomica.compatibility.Requirement
-
- isSatisfied(FeatureSet) - Method in class etomica.compatibility.RequirementSet
-
- isSelected(String) - Method in class etomica.graphics.DeviceButtonGroup
-
Returns true if the button of the given label is selected.
- isSelectMode - Variable in class etomica.normalmode.MCMoveHarmonic
-
- isShapeSecondary(int) - Static method in class org.jmol.viewer.JmolConstants
-
- isShowBorder() - Method in class etomica.graphics.DeviceSlider
-
- isShowBorder() - Method in class etomica.graphics.DeviceSpinner
-
- isShowingColumnHeaders() - Method in class etomica.graphics.DisplayTable
-
- isShowingRowLabels() - Method in class etomica.graphics.DisplayTable
-
Accessor method for flag indicating if table should include a column of
"x" values.
- isShowingUnits() - Method in class etomica.graphics.DisplayTable
-
- isSingleThreaded() - Method in interface org.jmol.api.ApiPlatform
-
- isSingleThreaded() - Method in class org.jmol.awt.Platform
-
- isSpecies1AtomicFlag() - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- isSpecies2AtomicFlag() - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- isSpeciesAlreadyAdded(int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- isSpeciesSelectionChanged() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- isSPP(BigInteger, BigInteger) - Method in class etomica.veos.bigdecimal.Prime
-
Test whether a number n is a strong pseudoprime to base a.
- issquare() - Method in class etomica.veos.bigdecimal.Ifactor
-
Test whether this is a square of an integer (perfect square).
- isStationary() - Method in class etomica.potential.P1HardMovingBoundary
-
- isStopSimulation() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- isStringArray(String) - Static method in class org.jmol.util.Escape
-
- isThermalEllipsoid - Variable in class org.jmol.util.Quadric
-
- isThermostatNoDrift() - Method in class etomica.integrator.IntegratorMD
-
- isTransposed() - Method in class etomica.graphics.DisplayTable
-
If true, each data set fills a row; if false, data are arranged to fill
columns.
- isTrial - Variable in class etomica.virial.BoxCluster
-
- isTriangleSet - Variable in class org.jmol.util.MeshSurface
-
- iSubstep - Variable in class etomica.thermointegration.IntegratorThermodynamic
-
- isUnitQuaternion() - Method in class etomica.math.Quaternion
-
Returns whether the norm of the Quaternion is 1 or not
- isUpdatingOnAnyChange() - Method in class etomica.data.DataSet
-
- isUpperBound - Variable in class etomica.modules.multiharmonic.DataProcessorBounds
-
- iSurf - Variable in class etomica.potential.P2WaterPotentialsJankowski
-
- iSurf - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- isUsePermutations() - Method in class etomica.virial.ClusterBonds
-
Returns the usePermutations flag.
- isValid(double[][][]) - Method in interface etomica.virial.ClusterSumAssociation.ClusterCriteria
-
- isValueProperty() - Method in class etomica.meta.properties.ArrayProperty
-
Gets the value of the property valueProperty.
- isValueProperty() - Method in class etomica.meta.properties.AtomListProperty
-
Gets the value of the property valueProperty.
- isValueProperty() - Method in class etomica.meta.properties.InstanceProperty
-
Gets the value of the property valueProperty.
- isValueProperty() - Method in class etomica.meta.properties.MoleculeListProperty
-
Gets the value of the property valueProperty.
- isValueProperty() - Method in interface etomica.meta.properties.Property
-
Gets the value of the property valueProperty.
- isValueProperty() - Method in class etomica.meta.properties.VectorProperty
-
Gets the value of the property valueProperty.
- isVariableType(Object) - Static method in class org.jmol.script.ScriptVariable
-
- isVolFluctuation() - Method in class etomica.models.nitrogen.MeterNormalizedCoord
-
- isWild(String) - Static method in class org.jmol.util.TextFormat
-
- isWithin(Point3f) - Method in class org.jmol.util.BoxInfo
-
- isWriteable(File) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Checks if the application is allowed to write to the file.
- isWriteOnInterval() - Method in class etomica.data.DataLogger
-
- isXComp() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- isXFlipped() - Method in class g3dsys.control.G3DSys
-
- isYComp() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- isYFlipped() - Method in class g3dsys.control.G3DSys
-
- isyst - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- isZero() - Method in interface etomica.space.Vector
-
Returns true if all components of this vector are zero; false otherwise.
- isZero() - Method in class etomica.space1d.Vector1D
-
- isZero() - Method in class etomica.space2d.Vector2D
-
- isZero() - Method in class etomica.space3d.Vector3D
-
- isZero() - Method in class etomica.spaceNd.VectorND
-
- isZero() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Test whether this polynomial value is zero.
- isZero() - Method in class etomica.veos.BigValue
-
- isZero() - Method in interface etomica.veos.IBigValue
-
Returns true if this instance has a value of zero.
- isZero() - Method in class etomica.veos.MyBigDecimal
-
- iT - Variable in class etomica.potential.PotentialCalculationPhiSum
-
- iTag - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- iTemperatureStep - Variable in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- itemStateChanged(ItemEvent) - Method in class etomica.graphics.DimensionedDoubleEditor
-
ItemListener interface implementation.
- itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.BondInteractionTypeToggler
-
- itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.BondTypeToggler
-
- itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ConnectedToggler
-
- itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.GraphicsToggler
-
- itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.NumbersToggler
-
- itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.PointsToggler
-
- itemStateChanged(ItemEvent) - Method in class etomica.modules.clustergenerator.MyApplet.ReeHooverToggler
-
- itemStateChanged(ItemEvent) - Method in class etomica.modules.joulethomson.JouleThomson.SpeciesChooser
-
- iterator - Variable in class etomica.data.meter.MeterDihedralAngle
-
- iterator - Variable in class etomica.data.meter.MeterRDF
-
- iterator - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- iterator() - Method in class etomica.graph.model.GraphList
-
- Iterator(int) - Constructor for class etomica.lattice.RectangularLattice.Iterator
-
- iterator - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- iterator - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- iterator - Variable in class etomica.normalmode.MCMoveHarmonic
-
- iterator - Variable in class etomica.normalmode.MCMoveHarmonicStep
-
- iterator - Variable in class etomica.potential.PotentialGroup.PotentialLinker
-
- iterator - Variable in class etomica.potential.PotentialMaster.PotentialLinker
-
- iteratorDirective - Variable in class etomica.data.meter.MeterHyperVirial
-
- iteratorDirective - Variable in class etomica.data.meter.MeterPotentialEnergy
-
- iteratorDirective - Variable in class etomica.data.meter.MeterPressureTensor
-
- iteratorDirective - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- iteratorDirective - Variable in class etomica.liquidLJ.MeterPU
-
- iteratorDirective - Variable in class etomica.liquidLJ.MeterPUCut
-
- iteratorDirective - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- IteratorDirective - Class in etomica.potential
-
Encapsulation of a set of instructions that an AtomsetIterator
uses to select the atoms it presents on iteration.
- IteratorDirective() - Constructor for class etomica.potential.IteratorDirective
-
- IteratorDirective(IteratorDirective.Direction) - Constructor for class etomica.potential.IteratorDirective
-
- IteratorDirective(IteratorDirective.Direction, IAtom) - Constructor for class etomica.potential.IteratorDirective
-
- IteratorDirective(IteratorDirective.Direction, IMolecule) - Constructor for class etomica.potential.IteratorDirective
-
- IteratorDirective.Direction - Enum in etomica.potential
-
- IteratorEF(byte, boolean) - Constructor for class etomica.virial.PYGenerator.IteratorEF
-
- IteratorFactory - Class in etomica.molecule.iterator
-
Class for construction of iterators of molecules.
- IteratorFactory() - Constructor for class etomica.molecule.iterator.IteratorFactory
-
- iteratorFactory - Variable in class etomica.potential.PotentialMaster
-
- IteratorToSet - Class in etomica.graph.iterators
-
- IteratorToSet() - Constructor for class etomica.graph.iterators.IteratorToSet
-
- IteratorWrapper - Class in etomica.graph.iterators
-
- IteratorWrapper(Iterator<Graph>) - Constructor for class etomica.graph.iterators.IteratorWrapper
-
- IteratorWrapper(Iterator<Graph>, boolean) - Constructor for class etomica.graph.iterators.IteratorWrapper
-
- iThread - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- iThread - Variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- iThread - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- iThread - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- iThread - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- itypus - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- iValue(Token) - Static method in class org.jmol.script.ScriptVariable
-
- iweight - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- iy - Variable in class etomica.math.numerical.AkimaSplineSmootherDy
-
- M - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- m - Variable in class etomica.lattice.IndexIteratorIncreasing
-
- m - Variable in class etomica.math.numerical.AkimaSpline
-
- m - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- M - Variable in class etomica.math.numerical.FittingFunctionNonLinear
-
- m - Variable in class etomica.meam.PotentialEAM
-
- m - Variable in class etomica.meam.PotentialEAM_LS
-
- M - Static variable in class etomica.util.random.RandomMersenneTwister
-
- m - Variable in class etomica.virial.ClusterMultiToSingle
-
- m00 - Variable in class org.jmol.util.Matrix3f
-
The first element of the first row.
- m00 - Variable in class org.jmol.util.Matrix4f
-
The first element of the first row.
- m01 - Variable in class org.jmol.util.Matrix3f
-
The second element of the first row.
- m01 - Variable in class org.jmol.util.Matrix4f
-
The second element of the first row.
- m02 - Variable in class org.jmol.util.Matrix3f
-
third element of the first row.
- m02 - Variable in class org.jmol.util.Matrix4f
-
third element of the first row.
- m03 - Variable in class org.jmol.util.Matrix4f
-
The fourth element of the first row.
- m10 - Variable in class org.jmol.util.Matrix3f
-
The first element of the second row.
- m10 - Variable in class org.jmol.util.Matrix4f
-
The first element of the second row.
- m11 - Variable in class org.jmol.util.Matrix3f
-
The second element of the second row.
- m11 - Variable in class org.jmol.util.Matrix4f
-
The second element of the second row.
- m12 - Variable in class org.jmol.util.Matrix3f
-
The third element of the second row.
- m12 - Variable in class org.jmol.util.Matrix4f
-
The third element of the second row.
- m13 - Variable in class org.jmol.util.Matrix4f
-
The fourth element of the second row.
- m2 - Variable in class etomica.meam.P2EAM
-
- m20 - Variable in class org.jmol.util.Matrix3f
-
The first element of the third row.
- m20 - Variable in class org.jmol.util.Matrix4f
-
The first element of the third row.
- m21 - Variable in class org.jmol.util.Matrix3f
-
The second element of the third row.
- m21 - Variable in class org.jmol.util.Matrix4f
-
The second element of the third row.
- m22 - Variable in class org.jmol.util.Matrix3f
-
The third element of the third row.
- m22 - Variable in class org.jmol.util.Matrix4f
-
The third element of the third row.
- m23 - Variable in class org.jmol.util.Matrix4f
-
The fourth element of the third row.
- m2s(IMoleculeList) - Static method in class etomica.virial.ClusterSumMultibody
-
- m30 - Variable in class org.jmol.util.Matrix4f
-
The first element of the fourth row.
- m31 - Variable in class org.jmol.util.Matrix4f
-
The second element of the fourth row.
- m32 - Variable in class org.jmol.util.Matrix4f
-
The third element of the fourth row.
- m33 - Variable in class org.jmol.util.Matrix4f
-
The fourth element of the fourth row.
- MacrostateManager - Interface in etomica.tmmc
-
Interface for class that defines the macrostates.
- madMultipleBondSmallMaximum - Static variable in class org.jmol.viewer.JmolConstants
-
- MAGENTA - Static variable in class org.jmol.util.Colix
-
- main(String[]) - Static method in class etomica.AlkaneEH.CH4NVT
-
- main(String[]) - Static method in class etomica.AlkaneEH.DHS_NVT
-
- main(String[]) - Static method in class etomica.AlkaneEH.DLJ_NVT_1site
-
- main(String[]) - Static method in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- main(String[]) - Static method in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid
-
- main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp
-
- main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite
-
- main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp
-
- main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal
-
- main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite
-
- main(String[]) - Static method in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling
-
- main(String[]) - Static method in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- main(String[]) - Static method in class etomica.association.TestLJAssociationMC3D_NPT
-
- main(String[]) - Static method in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- main(String[]) - Static method in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- main(String[]) - Static method in class etomica.conjugategradient.ConjugateGradients
-
- main(String[]) - Static method in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- main(String[]) - Static method in class etomica.conjugategradient.SteepestDescent
-
- main(String[]) - Static method in class etomica.conjugategradient.TestFiniteDifferenceDerivative
-
- main(String[]) - Static method in class etomica.conjugategradient.TestNonLinearConjugateGradients
-
- main(String[]) - Static method in class etomica.data.AccumulatorAverageBootstrap
-
- main(String[]) - Static method in class etomica.data.AccumulatorAverageCollapsingLog
-
- main(String[]) - Static method in class etomica.data.DataSourceUniform
-
Main method to demonstrate and check class.
- main(String[]) - Static method in class etomica.densityofstate.CopyOfOrthogonalPolynomial
-
- main(String[]) - Static method in class etomica.densityofstate.DensityOfState
-
- main(String[]) - Static method in class etomica.densityofstate.DensityOfStatesPolynomial
-
- main(String[]) - Static method in class etomica.densityofstate.FerrenbergSwendsen
-
- main(String[]) - Static method in class etomica.densityofstate.OrthogonalPolynomial
-
- main(String[]) - Static method in class etomica.dielectric.DHS_NVT
-
- main(String[]) - Static method in class etomica.dielectric.DLJ_NVT_1site
-
- main(String[]) - Static method in class etomica.dielectric.TIP4P_NVT
-
- main(String[]) - Static method in class etomica.dimer.EnergyMap
-
- main(String[]) - Static method in class etomica.dimer.EnergyMapCluster
-
- main(String[]) - Static method in class etomica.dimer.SimDimerLJadatom
-
- main(String[]) - Static method in class etomica.dimer.SimDimerLJadatomCluster
-
- main(String[]) - Static method in class etomica.dimer.SimDimerLJgb
-
- main(String[]) - Static method in class etomica.dimer.SimDimerMEAMadatom
-
- main(String[]) - Static method in class etomica.dimer.SimDimerMEAMadatomCluster
-
- main(String[]) - Static method in class etomica.dimer.SimDimerMEAMGB
-
- main(String[]) - Static method in class etomica.dimer.SimDimerMEAMGBCluster
-
- main(String[]) - Static method in class etomica.eigenstuff.ReaderIn
-
- main(String[]) - Static method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS
-
- main(String[]) - Static method in class etomica.freeenergy.npath.SimFe
-
- main(String[]) - Static method in class etomica.freeenergy.npath.SimIdealGas
-
- main(String[]) - Static method in class etomica.freeenergy.npath.SimLattice
-
- main(String[]) - Static method in class etomica.freeenergy.npath.SimLJ
-
- main(String[]) - Static method in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- main(String[]) - Static method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- main(String[]) - Static method in class etomica.graph.engine.Launcher
-
- main(String[]) - Static method in class etomica.graph.operations.DropOrphanNodes
-
- main(String[]) - Static method in class etomica.graph.property.FFTDecomposition
-
- main(String[]) - Static method in class etomica.graph.property.IsFFT
-
- main(String[]) - Static method in class etomica.graph.util.GraphNumber
-
- Main - Class in etomica.graph.view.rasterizer
-
Handles command line parameters to configure the SVGConverter
and rasterizer images.
- Main(String[]) - Constructor for class etomica.graph.view.rasterizer.Main
-
- main(String[]) - Static method in class etomica.graph.view.rasterizer.Main
-
- main(String[]) - Static method in class etomica.graphics.ColorScheme
-
- main(String[]) - Static method in class etomica.graphics.DeviceButton
-
Method to demonstrate and test the use of this class.
- main(String[]) - Static method in class etomica.graphics.DeviceNSelector
-
- main(String[]) - Static method in class etomica.graphics.DeviceTable
-
main method to demonstrate and test this class.
- main(String[]) - Static method in class etomica.graphics.DeviceThermoSelector
-
- main(String[]) - Static method in class etomica.graphics.DeviceThermoSlider
-
- main(String[]) - Static method in class etomica.graphics.DeviceToggleButton
-
Method to demonstrate and test the use of this class.
- main(String[]) - Static method in class etomica.graphics.DeviceTrioControllerButton
-
main method to show how to work with this class
- main(String[]) - Static method in class etomica.graphics.DisplayTable
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.graphics.DisplayTextBoxesCAE
-
- main(String[]) - Static method in class etomica.graphics.SimulationGraphic
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.integrator.IntegratorRigidIterative
-
- main(String[]) - Static method in class etomica.interfacial.LJMC
-
- main(String[]) - Static method in class etomica.interfacial.LJMD
-
- main(String[]) - Static method in class etomica.kmc.SimKMCLJadatom
-
- main(String[]) - Static method in class etomica.kmc.SimKMCmaster
-
- main(String[]) - Static method in class etomica.kmc.SimKMCMEAMadatom
-
- main(String[]) - Static method in class etomica.kmc.SimKMCworker
-
- main(String[]) - Static method in class etomica.lattice.crystal.PrimitiveFcc
-
- main(String[]) - Static method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- main(String[]) - Static method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- main(String[]) - Static method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- main(String[]) - Static method in class etomica.lattice.IndexIteratorIncreasing
-
- main(String[]) - Static method in class etomica.lattice.IndexIteratorRectangular
-
main method to test and demonstrate class.
- main(String[]) - Static method in class etomica.lattice.IndexIteratorReflecting
-
Method to test and demonstrate class.
- main(String[]) - Static method in class etomica.lattice.IndexIteratorTriangular
-
Method to test and demonstrate class.
- main(String[]) - Static method in class etomica.lattice.IndexIteratorTriangularPermutations
-
Method to test and demonstrate class.
- main(String[]) - Static method in class etomica.lattice.RectangularLatticeNbrIteratorAdjacent
-
Method to test the neighbor iterator.
- main(String[]) - Static method in class etomica.lattice.RectangularLatticeNbrIteratorSquare
-
Method to test the neighbor iterator.
- main(String[]) - Static method in class etomica.liquidLJ.LjMC3D
-
- main(String[]) - Static method in class etomica.liquidLJ.LjMd3D
-
- main(String[]) - Static method in class etomica.liquidLJ.LjMd3Dv2y
-
- Main - Class in etomica
-
- Main() - Constructor for class etomica.Main
-
- main(String[]) - Static method in class etomica.Main
-
- main(String[]) - Static method in class etomica.mappedRdf.MappedRdf
-
- main(String[]) - Static method in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- main(String[]) - Static method in class etomica.mappedvirial.MappedU
-
- main(String[]) - Static method in class etomica.mappedvirial.MappedVirialLJ
-
- main(String[]) - Static method in class etomica.mappedvirial.MappedVirialLJVGr
-
- main(String[]) - Static method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- main(String[]) - Static method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- main(String[]) - Static method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- main(String[]) - Static method in class etomica.math.discrete.CombinationIterator
-
- main(String[]) - Static method in class etomica.math.discrete.FixedSumIterator
-
- main(String[]) - Static method in class etomica.math.discrete.PermutationDegenerateIterator
-
- main(String[]) - Static method in class etomica.math.discrete.PermutationIterator
-
- main(String[]) - Static method in class etomica.math.Gamma
-
- main(String[]) - Static method in class etomica.math.geometry.LineSegment
-
- main(String[]) - Static method in class etomica.math.geometry.Plane
-
- main(String[]) - Static method in class etomica.math.numerical.AkimaSpline
-
- main(String[]) - Static method in class etomica.math.numerical.AkimaSplineSmootherApp
-
- main(String[]) - Static method in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- main(String[]) - Static method in class etomica.math.numerical.AkimaSplineSmootherMain
-
- main(String[]) - Static method in class etomica.math.numerical.FastFourierTransform
-
- main(String[]) - Static method in class etomica.math.numerical.LinearFit
-
- main(String[]) - Static method in class etomica.math.numerical.PadeApproximation
-
- main(String[]) - Static method in class etomica.math.numerical.PolynomialFit
-
- main(String[]) - Static method in class etomica.math.numerical.VirialOptimizer
-
- main(String[]) - Static method in class etomica.math.SpecialFunctions
-
- main(String[]) - Static method in class etomica.meam.EFSTungsten
-
- main(String[]) - Static method in class etomica.meam.MEAM_3DMDwithGB
-
- main(String[]) - Static method in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- main(String[]) - Static method in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- main(String[]) - Static method in class etomica.meam.MEAM_MC
-
- main(String[]) - Static method in class etomica.meam.MEAMMd3D
-
- main(String[]) - Static method in class etomica.meam.MEAMMd3DforCluster
-
- main(String[]) - Static method in class etomica.meta.DataSourceIndex
-
- main(String[]) - Static method in class etomica.metastable.LJmuVT
-
- main(String[]) - Static method in class etomica.metastable.LJNPT
-
- main(String[]) - Static method in class etomica.metastable.LJNVT
-
- main(String[]) - Static method in class etomica.models.clathrates.ClathrateHarmonicFE
-
- main(String[]) - Static method in class etomica.models.clathrates.MinimizationTIP4P
-
- main(String[]) - Static method in class etomica.models.co2.P2CO2H2OWheatley
-
Randomly moves molcules all over, computing and checking 2nd derivative
- main(String[]) - Static method in class etomica.models.co2.P2CO2Hellmann
-
- main(String[]) - Static method in class etomica.models.co2.PNCO2GCPM
-
- main(String[]) - Static method in class etomica.models.co2.PNGCPM
-
- main(String[]) - Static method in class etomica.models.hexane.HexaneVolumeFraction
-
- main(String[]) - Static method in class etomica.models.hexane.SimHarmonicHexane
-
- main(String[]) - Static method in class etomica.models.hexane.TestHexane
-
- main(String[]) - Static method in class etomica.models.hexane.TestHexaneCBMCOnly
-
- main(String[]) - Static method in class etomica.models.hexane.TestHexaneFileConfig
-
- main(String[]) - Static method in class etomica.models.hexane.TestHexaneHarmonic
-
- main(String[]) - Static method in class etomica.models.hexane.TestSetToUHexane
-
- main(String[]) - Static method in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
-
- main(String[]) - Static method in class etomica.models.nitrogen.FindTransitionTemperature
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelLatticeSum
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelLatticeSum
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- main(String[]) - Static method in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- main(String[]) - Static method in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- main(String[]) - Static method in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- main(String[]) - Static method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- main(String[]) - Static method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- main(String[]) - Static method in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- main(String[]) - Static method in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- main(String[]) - Static method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimDirectBetaN2RP
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- main(String[]) - Static method in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- main(String[]) - Static method in class etomica.models.nitrogen.TestRotationVector
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.DoubleIntegral
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.DoubleIntegralEtas
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.HarmonicCrystalSsFccBigCellNxy
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.HarmonicCrystalSsFccDoubleSize
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.MakeData
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimDegFreeBinning
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimDegreeFreedom
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimDegreeFreedom3D
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImage
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimExtensiveTest
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.SimWidomMode
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- main(String[]) - Static method in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- main(String[]) - Static method in class etomica.models.rowley.DimerApproach
-
- main(String[]) - Static method in class etomica.models.rowley.MassProductionVirialRowleyAlcohol
-
- main(String[]) - Static method in class etomica.models.water.P2WaterSzalewicz
-
- main(String[]) - Static method in class etomica.models.water.TestEwaldTIP4PWater
-
- main(String[]) - Static method in class etomica.modules.adsorption.Adsorption
-
- main(String[]) - Static method in class etomica.modules.adsorption.AdsorptionGraphic
-
- main(String[]) - Static method in class etomica.modules.catalysis.Catalysis
-
- main(String[]) - Static method in class etomica.modules.catalysis.CatalysisGraphic
-
- main(String[]) - Static method in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
-
- main(String[]) - Static method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
-
- main(String[]) - Static method in class etomica.modules.colloid.ColloidGraphic
-
- main(String[]) - Static method in class etomica.modules.colloid.ColloidSim
-
- main(String[]) - Static method in class etomica.modules.crystalviewer.CrystalViewer
-
- main(String[]) - Static method in class etomica.modules.dcvgcmd.DCVGCMDGraphic
-
- main(String[]) - Static method in class etomica.modules.droplet.Droplet
-
- main(String[]) - Static method in class etomica.modules.droplet.DropletAtomic
-
- main(String[]) - Static method in class etomica.modules.droplet.DropletAtomicGraphic
-
- main(String[]) - Static method in class etomica.modules.droplet.DropletGraphic
-
- main(String[]) - Static method in class etomica.modules.ensembles.LJMC
-
- main(String[]) - Static method in class etomica.modules.ensembles.LJMCGraphic
-
- main(String[]) - Static method in class etomica.modules.entropylottery.EntropyLottery
-
- main(String[]) - Static method in class etomica.modules.entropylottery.EntropyLotteryGraphic
-
- main(String[]) - Static method in class etomica.modules.insertion.Insertion
-
- main(String[]) - Static method in class etomica.modules.insertion.InsertionGraphic
-
- main(String[]) - Static method in class etomica.modules.interfacial.FitTanh
-
- main(String[]) - Static method in class etomica.modules.interfacial.InterfacialSW
-
- main(String[]) - Static method in class etomica.modules.interfacial.InterfacialSWGraphic
-
- main(String[]) - Static method in class etomica.modules.joulethomson.JouleThomson
-
- main(String[]) - Static method in class etomica.modules.joulethomson.JouleThomsonSim
-
- main(String[]) - Static method in class etomica.modules.ljmd.Ljmd
-
- main(String[]) - Static method in class etomica.modules.ljmd.LjmdGraphic
-
- main(String[]) - Static method in class etomica.modules.materialfracture.MaterialFractureGraphic
-
/* main method
- main(String[]) - Static method in class etomica.modules.mu.Mu
-
- main(String[]) - Static method in class etomica.modules.mu.MuGraphic
-
- main(String[]) - Static method in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
-
- main(String[]) - Static method in class etomica.modules.multiharmonic.MultiharmonicGraphic
-
- main(String[]) - Static method in class etomica.modules.multiharmonic.MultiharmonicGraphicMC
-
- main(String[]) - Static method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- main(String[]) - Static method in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
-
- main(String[]) - Static method in class etomica.modules.osmosis.Osmosis
-
- main(String[]) - Static method in class etomica.modules.osmosis.OsmosisSim
-
- main(String[]) - Static method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- main(String[]) - Static method in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
-
- main(String[]) - Static method in class etomica.modules.render.ParseObj
-
- main(String[]) - Static method in class etomica.modules.render.RenderMDGraphic
-
- main(String[]) - Static method in class etomica.modules.rheology.RheologyGraphic
-
- main(String[]) - Static method in class etomica.modules.rheology.SimulationRheology
-
- main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosis
-
- main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- main(String[]) - Static method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- main(String[]) - Static method in class etomica.modules.sam.Sam
-
- main(String[]) - Static method in class etomica.modules.sam.SamGraphic
-
- main(String[]) - Static method in class etomica.modules.statistics.StatisticsMCGraphic
-
- main(String[]) - Static method in class etomica.modules.swmd.Swmd
-
- main(String[]) - Static method in class etomica.modules.swmd.SwmdGraphic
-
- main(String[]) - Static method in class etomica.modules.vle.B2Fit
-
- main(String[]) - Static method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- main(String[]) - Static method in class etomica.modules.vle.LJQB2
-
- main(String[]) - Static method in class etomica.modules.vle.VLE
-
- main(String[]) - Static method in class etomica.modules.vle.VLESim
-
- main(String[]) - Static method in class etomica.normalmode.ArrayA2B
-
- main(String[]) - Static method in class etomica.normalmode.ArrayB2A
-
- main(String[]) - Static method in class etomica.normalmode.CalcHarmonicA
-
- main(String[]) - Static method in class etomica.normalmode.DeviceCellNum3DSlider
-
- main(String[]) - Static method in class etomica.normalmode.DeviceCellNumXYSlider
-
- main(String[]) - Static method in class etomica.normalmode.DeviceEigenvaluesSlider
-
- main(String[]) - Static method in class etomica.normalmode.DeviceWaveVectorSlider
-
- main(String[]) - Static method in class etomica.normalmode.HarmonicCrystal
-
- main(String[]) - Static method in class etomica.normalmode.HarmonicCrystalSoftSphereBCC
-
- main(String[]) - Static method in class etomica.normalmode.HarmonicCrystalSoftSphereFCC
-
- main(String[]) - Static method in class etomica.normalmode.HarmonicCrystalSoftSphereHCP
-
- main(String[]) - Static method in class etomica.normalmode.HarmonicCrystalSsFccNxy
-
- main(String[]) - Static method in class etomica.normalmode.HessianDB
-
- main(String[]) - Static method in class etomica.normalmode.HessianFromFile
-
- main(String[]) - Static method in class etomica.normalmode.HSDimerNPT
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.normalmode.HSNPT
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.normalmode.HTTPSoftSphereApplet
-
- main(String[]) - Static method in class etomica.normalmode.LJVacancyMin
-
- main(String[]) - Static method in class etomica.normalmode.MeterHarmonicEnergy
-
- main(String[]) - Static method in class etomica.normalmode.MinimizeHCP
-
- main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- main(String[]) - Static method in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- main(String[]) - Static method in class etomica.normalmode.NormalModeEigenGetter
-
- main(String[]) - Static method in class etomica.normalmode.NormalModes1DHR
-
- main(String[]) - Static method in class etomica.normalmode.NormalModes3D
-
- main(String[]) - Static method in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.normalmode.SimBennet
-
- main(String[]) - Static method in class etomica.normalmode.SimCalcJ
-
- main(String[]) - Static method in class etomica.normalmode.SimCalcS
-
- main(String[]) - Static method in class etomica.normalmode.SimCalcSLJ
-
- main(String[]) - Static method in class etomica.normalmode.SimCalcSMorse
-
- main(String[]) - Static method in class etomica.normalmode.SimCalcSSoftSphere2D
-
- main(String[]) - Static method in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- main(String[]) - Static method in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- main(String[]) - Static method in class etomica.normalmode.SimEinStep1
-
- main(String[]) - Static method in class etomica.normalmode.SimEinStep1HCP
-
- main(String[]) - Static method in class etomica.normalmode.SimEinStep2
-
- main(String[]) - Static method in class etomica.normalmode.SimEinStep2HCP
-
- main(String[]) - Static method in class etomica.normalmode.SimFluidSoftSphere
-
- main(String[]) - Static method in class etomica.normalmode.SimHarmonic
-
- main(String[]) - Static method in class etomica.normalmode.SimHarmonicUmbrella
-
- main(String[]) - Static method in class etomica.normalmode.SimHSMDVacancy
-
- main(String[]) - Static method in class etomica.normalmode.SimLJHTTISuper
-
- main(String[]) - Static method in class etomica.normalmode.SimLJHTTISuperHCP
-
- main(String[]) - Static method in class etomica.normalmode.SimLJVacancy
-
- main(String[]) - Static method in class etomica.normalmode.SimModesJ
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlap
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapLJ
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapLJModule
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphere
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereDP
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereEin
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereTP
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- main(String[]) - Static method in class etomica.normalmode.SimOverlapSSnxy
-
- main(String[]) - Static method in class etomica.normalmode.SimTarget
-
- main(String[]) - Static method in class etomica.normalmode.SimTargetUmbrella
-
- main(String[]) - Static method in class etomica.normalmode.SimUmbrella
-
- main(String[]) - Static method in class etomica.normalmode.SimUmbrellaSoftSphere
-
- main(String[]) - Static method in class etomica.normalmode.SoftSphereSolidEOS
-
- main(String[]) - Static method in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- main(String[]) - Static method in class etomica.normalmode.WaveVectorFactory1D
-
- main(String[]) - Static method in class etomica.normalmode.WaveVectorFactory2D
-
- main(String[]) - Static method in class etomica.normalmode.WaveVectorFactoryFcc
-
- main(String[]) - Static method in class etomica.normalmode.WaveVectorFactorySimple
-
- main(String[]) - Static method in class etomica.paracetamol.HarmonicCrystalMonoclinic
-
- main(String[]) - Static method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
-
- main(String[]) - Static method in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- main(String[]) - Static method in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTIEquilibration
-
- main(String[]) - Static method in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTISimCalcS
-
- main(String[]) - Static method in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- main(String[]) - Static method in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTIEquilibration
-
- main(String[]) - Static method in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTISimCalcS
-
- main(String[]) - Static method in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- main(String[]) - Static method in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- main(String[]) - Static method in class etomica.paracetamol.MDParacetamolMonoclinic
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.paracetamol.MDParacetamolOrthorhombic
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.paracetamol.NormalModeEigenGetter
-
- main(String[]) - Static method in class etomica.parser.ParserLAMMPS
-
- main(String[]) - Static method in class etomica.potential.P2ArgonSlavicekEtAl2003
-
- main(String[]) - Static method in class etomica.potential.P2ArgonTangAndToennies2003
-
- main(String[]) - Static method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- main(String[]) - Static method in class etomica.potential.P2EffectiveFeynmanHibbs
-
- main(String[]) - Static method in class etomica.potential.P2HePCKLJS
-
- main(String[]) - Static method in class etomica.potential.P2HydrogenHinde
-
- main(String[]) - Static method in class etomica.potential.P2HydrogenPatkowski
-
- main(String[]) - Static method in class etomica.potential.P2HydrogenPatkowskiIso
-
- main(String[]) - Static method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- main(String[]) - Static method in class etomica.potential.P2NitrogenHellmann
-
- main(String[]) - Static method in class etomica.potential.P2O2Bartolomei
-
- main(String[]) - Static method in class etomica.potential.P2QChemInterpolated
-
- main(String[]) - Static method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- main(String[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- main(String[]) - Static method in class etomica.potential.P3AdditiveQChem
-
- main(String[]) - Static method in class etomica.potential.P3BondAngle
-
- main(String[]) - Static method in class etomica.potential.P3CPSNonAdditiveHe
-
- main(String[]) - Static method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- main(String[]) - Static method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- main(String[]) - Static method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- main(String[]) - Static method in class etomica.potential.P3HydrogenATM
-
- main(String[]) - Static method in class etomica.potential.P3HydrogenManzhos
-
- main(String[]) - Static method in class etomica.potential.P3Induction
-
- main(String[]) - Static method in class etomica.potential.P3QChem
-
- main(String[]) - Static method in class etomica.potential.P4BondTorsion
-
- main(String[]) - Static method in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- main(String[]) - Static method in class etomica.potential.P4BondTorsionOPLS
-
- main(String[]) - Static method in class etomica.potential.PotentialEmul
-
- main(String[]) - Static method in class etomica.rotation.DipoleBox
-
- main(String[]) - Static method in class etomica.rotation.DipoleBoxMatrix
-
- main(String[]) - Static method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- main(String[]) - Static method in class etomica.rotation.P2LJDipole
-
- main(String[]) - Static method in class etomica.rotation.SingleDipole
-
- main(String[]) - Static method in class etomica.rotation.SingleDumbellRattle
-
- main(String[]) - Static method in class etomica.rotation.SingleDumbellShake
-
- main(String[]) - Static method in class etomica.rotation.SingleWater
-
- main(String[]) - Static method in class etomica.rotation.SingleWaterMatrix
-
- main(String[]) - Static method in class etomica.rotation.SingleWaterRattle
-
- main(String[]) - Static method in class etomica.rotation.SingleWaterShake
-
- main(String[]) - Static method in class etomica.rotation.WaterBox
-
- main(String[]) - Static method in class etomica.rotation.WaterDroplet
-
- main(String[]) - Static method in class etomica.rotation.WaterDropletMatrix
-
- main(String[]) - Static method in class etomica.rotation.WaterDropletRattle
-
- main(String[]) - Static method in class etomica.rotation.WaterDropletShake
-
- main(String[]) - Static method in class etomica.rotation.WaterTrimer
-
- main(String[]) - Static method in class etomica.rotation.WaterTrimerRattle
-
- main(String[]) - Static method in class etomica.rotation.WaterTrimerShake
-
- main(String[]) - Static method in class etomica.server.EtomicaServer
-
- main(String[]) - Static method in class etomica.simulation.BenchSimSWChain
-
- main(String[]) - Static method in class etomica.simulation.prototypes.ChainHSMD3D
-
- main(String[]) - Static method in class etomica.simulation.prototypes.GEMCWithRotation
-
- main(String[]) - Static method in class etomica.simulation.prototypes.HSMC2D
-
- main(String[]) - Static method in class etomica.simulation.prototypes.HSMD2D
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.simulation.prototypes.HSMD2D_noNbr
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.simulation.prototypes.HSMD3D
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.simulation.prototypes.HSMD3DNoNbr
-
- main(String[]) - Static method in class etomica.simulation.prototypes.LJMD3D
-
- main(String[]) - Static method in class etomica.simulation.prototypes.SoftSphere3d
-
- main(String[]) - Static method in class etomica.simulation.prototypes.SWMD3D
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.space.BenchVector3D
-
- main(String[]) - Static method in class etomica.space3d.RotationTensor3D
-
Method to test rotation tensor.
- main(String[]) - Static method in class etomica.spin.Heisenberg
-
- main(String[]) - Static method in class etomica.statmech.HardSphere
-
- main(String[]) - Static method in class etomica.statmech.HardSphereSolid
-
- main(String[]) - Static method in class etomica.statmech.LennardJones
-
- main(String[]) - Static method in class etomica.surfacetension.FitTanh
-
- main(String[]) - Static method in class etomica.surfacetension.LJMC
-
- main(String[]) - Static method in class etomica.tests.TestHSMD3D
-
Demonstrates how this class is implemented.
- main(String[]) - Static method in class etomica.tests.TestLJGCMC3D
-
- main(String[]) - Static method in class etomica.tests.TestLJMC3D
-
- main(String[]) - Static method in class etomica.tests.TestSWChain
-
- main(String[]) - Static method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- main(String[]) - Static method in class etomica.thermointegration.LjMc3D
-
- main(String[]) - Static method in class etomica.threaded.atom.LJMD3DThreaded
-
- main(String[]) - Static method in class etomica.threaded.atom.LJMD3DThreadedforCluster
-
- main(String[]) - Static method in class etomica.threaded.domain.LJMD3DThreaded
-
- main(String[]) - Static method in class etomica.threaded.domain.LJMD3DThreadedforCluster
-
- main(String[]) - Static method in class etomica.threaded.domain.MEAMMd3DThreaded
-
- main(String[]) - Static method in class etomica.threaded.domain.MEAMMd3DThreadedforCluster
-
- main(String[]) - Static method in class etomica.threads.AtomDecompositionMD
-
- main(String[]) - Static method in class etomica.units.gui.UnitFilter
-
- main(String[]) - Method in class etomica.units.gui.UnitGraphics
-
- main(String[]) - Static method in class etomica.util.Constants
-
- main(String[]) - Static method in class etomica.util.Grabber
-
- main(String[]) - Static method in class etomica.util.random.RandomNumberGeneratorUnix
-
- main(String[]) - Static method in class etomica.util.ReadParameters
-
- main(String[]) - Static method in class etomica.util.ScientificFormat
-
- main(String[]) - Static method in class etomica.util.Strings
-
- main(String[]) - Static method in class etomica.veos.bigdecimal.EulerPhi
-
Test program.
- main(String[]) - Static method in class etomica.veos.bigdecimal.Ifactor
-
Test program.
- main(String[]) - Static method in class etomica.veos.bigdecimal.PartitionsP
-
Test program.
- main(String[]) - Static method in class etomica.veos.bigdecimal.Prime
-
Test program.
- main(String[]) - Static method in class etomica.veos.bigdecimal.Wigner3j
-
Test programs.
- main(String[]) - Static method in class etomica.veos.bigdecimal.Wigner3jGUI
-
Main entry point.
- main(String[]) - Static method in class etomica.veos.BigValue
-
- main(String[]) - Static method in class etomica.veos.MyBigDecimal
-
- main(String[]) - Static method in class etomica.veos.QSeries
-
- main(String[]) - Static method in class etomica.veos.Ushcats
-
- main(String[]) - Static method in class etomica.virial.B2ForSphericallySymmetricUByTrapezoidRule
-
- main(String[]) - Static method in class etomica.virial.B2Ionic
-
- main(String[]) - Static method in class etomica.virial.B3ForSphericallySymmetricU
-
- main(String[]) - Static method in class etomica.virial.B3LJ
-
- main(String[]) - Static method in class etomica.virial.B3NonAddForSphericallySymmetricU
-
- main(String[]) - Static method in class etomica.virial.B4FFTLJ
-
- main(String[]) - Static method in class etomica.virial.B5FFTLJ
-
- main(String[]) - Static method in class etomica.virial.B6FFTLJ
-
- main(String[]) - Static method in class etomica.virial.BnHNCLJ
-
- main(String[]) - Static method in class etomica.virial.BnHSIonic
-
- main(String[]) - Static method in class etomica.virial.BnIETP2Spherical
-
- main(String[]) - Static method in class etomica.virial.BnJHBVArgon_Analytic
-
- main(String[]) - Static method in class etomica.virial.BnPY_1QC_Helium
-
- main(String[]) - Static method in class etomica.virial.BnPYCHe
-
- main(String[]) - Static method in class etomica.virial.BnPYHardSphere
-
- main(String[]) - Static method in class etomica.virial.BnPYLJ
-
- main(String[]) - Static method in class etomica.virial.BnSCALJ
-
- main(String[]) - Static method in class etomica.virial.CalcFFT
-
- main(String[]) - Static method in class etomica.virial.cluster.ClusterDiagram
-
- main(String[]) - Static method in class etomica.virial.cluster.ClusterGenerator
-
Demonstrates how to use this class.
- main(String[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
- main(String[]) - Static method in class etomica.virial.cluster.DCF
-
- main(String[]) - Static method in class etomica.virial.cluster.ExternalVirialDiagrams
-
- main(String[]) - Static method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- main(String[]) - Static method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- main(String[]) - Static method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- main(String[]) - Static method in class etomica.virial.cluster.PermutationIterator
-
- main(String[]) - Static method in class etomica.virial.cluster.Standard
-
- main(String[]) - Static method in class etomica.virial.cluster.VirialDiagrams
-
- main(String[]) - Static method in class etomica.virial.cluster.VirialDiagramsMix
-
- main(String[]) - Static method in class etomica.virial.cluster.VirialDiagramsMix2
-
- main(String[]) - Static method in class etomica.virial.cluster.VirialDiagramsPT
-
- main(String[]) - Static method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- main(String[]) - Static method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- main(String[]) - Static method in class etomica.virial.ClusterBonds
-
- main(String[]) - Static method in class etomica.virial.ClusterChainHS
-
- main(String[]) - Static method in class etomica.virial.ClusterSinglyConnected
-
- main(String[]) - Static method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- main(String[]) - Static method in class etomica.virial.GUI.ApplicationMixtureBuilder
-
- main(String[]) - Static method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- main(String[]) - Static method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- main(String[]) - Static method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- main(String[]) - Static method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- main(String[]) - Static method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- main(String[]) - Static method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- main(String[]) - Static method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- main(String[]) - Static method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- main(String[]) - Static method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- main(String[]) - Static method in class etomica.virial.HNCGenerator
-
- main(String[]) - Static method in class etomica.virial.IsFFT
-
- main(String[]) - Static method in class etomica.virial.MCMoveClusterAtomHSRing
-
- main(String[]) - Static method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- main(String[]) - Static method in class etomica.virial.PotentialNonAdditive
-
- main(String[]) - Static method in class etomica.virial.PYGenerator
-
- main(String[]) - Static method in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol
-
- main(String[]) - Static method in class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr
-
- main(String[]) - Static method in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt
-
- main(String[]) - Static method in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt
-
- main(String[]) - Static method in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt
-
- main(String[]) - Static method in class etomica.virial.simulations.FourAssociationSitesFluid2Pt
-
- main(String[]) - Static method in class etomica.virial.simulations.LJTSRefLJ
-
- main(String[]) - Static method in class etomica.virial.simulations.ReeHooverMC
-
- main(String[]) - Static method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- main(String[]) - Static method in class etomica.virial.simulations.SimulationVirialUmbrella
-
- main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid
-
- main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid2
-
- main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt
-
- main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt
-
- main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid4Points
-
- main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt
-
- main(String[]) - Static method in class etomica.virial.simulations.SingleAssociationSiteFluidGraph
-
- main(String[]) - Static method in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- main(String[]) - Static method in class etomica.virial.simulations.Virial2CLJQ
-
- main(String[]) - Static method in class etomica.virial.simulations.Virial7SiteRigidSF6
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAceticAcid
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAceticAcidFlex
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAlkane
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneEHTest
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneFlex
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneFull
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneMix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneMix2
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneMix2_Kong
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneMix_Kong
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAlkaneSKS
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAnthracene464
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAnthracene545
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAnthraceneTraPPE
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAssociatingFluid
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialAssociatingFluid4points
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialB3C1HSDipole
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialB3C1TIP4Pwater
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialB3C2HSDipole
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialB3C2TIP4Pwater
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCH4AlkaneEHMix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2AlkaneEHMix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2AlkaneUAMix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2anthracene464
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2anthracene545
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2CH4Mix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2CH4UAMix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2H2OGCPM
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2H2OGCPMX
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2H2OSC
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2LJQ
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2N2Mix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2PI
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2SKSMix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCO2TraPPE
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCPSHeliumNonAdditive
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialEmulNonAdditive
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialExternalFieldOverlapRho
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialGCPM
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialGCPMGraphic
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialH2O
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialH2OGCPMD
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialH2PI
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialH2PIBoltzmann
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialH2PISimple
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialH2PIXC
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialH2PYCorrection
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHardAssociationCone
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHeNonAdditive
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHeNonAdditiveWheatley
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHePCKLJS
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHePCKLJSPYCorrection
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHePCKLJSTempDeriv
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHePI
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHePI_PotentialCorrection
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHePIGraphic
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHePIXC
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHePIXCEven
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHePIXCOdd
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHePYCorrection
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHeSC
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHS
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHSBinMultiThreaded
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHSMixture
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialHSOrC
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialLJ
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialLJBridge
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialLJCHNCCorrection
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialLJD
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialLJMultiOverlap
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialLJOrC
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialLJOrICPYC
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialLJPYCorrection
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialLJSeries
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialMethaneEH
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialN2
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialN2AlkaneEHMix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialN2AlkaneUAMix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialN2AlkaneUARigid
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialN2CH4Mix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialN2CH4UAMix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialN2PI
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialN2TraPPE
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialNaphthaleneTraPPE
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialO2
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialO2PI
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialPh464
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialPh545
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialPhenanthreneTraPPE
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialPolyhedra
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialPolyhedra2
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialRowleyAlcohol
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialSQWBinMultiRecalcW
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialSQWBinMultiThreaded
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialSQWRecalcSmallMem
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialSW
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialSwsPT
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialSWWE
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialTraPPEAlcohol
-
- main(String[]) - Static method in class etomica.virial.simulations.VirialWaterOverlap
-
- main(String[]) - Static method in class etomica.yukawa.TestHC2YukawaMC3D
-
- main(String[]) - Static method in class etomica.yukawa.TestYukawaMC3D
-
- main(String[]) - Static method in class etomica.yukawa.TestYukawaMD3D
-
- main(String[]) - Static method in class etomica.zeolite.DataCutter
-
- main(String[]) - Static method in class etomica.zeolite.DeviceButtonSingle
-
Method to demonstrate and test the use of this class.
- main(String[]) - Static method in class etomica.zeolite.Zeolite
-
- main(String[]) - Static method in class etomica.zeolite.ZeoliteSimulation
-
Demonstrates how this class is implemented.
- Main.AbstractOptionHandler - Class in etomica.graph.view.rasterizer
-
This abstract implementation of the OptionHandler interface
throws an exception if the number of arguments passed to the
handleOption method does not match the number of expected
optionValues.
- Main.ColorOptionHandler - Class in etomica.graph.view.rasterizer
-
Base class for options which expect a Color optionValue.
- Main.FloatOptionHandler - Class in etomica.graph.view.rasterizer
-
Base class for options which expect the single optionValue to
be a float.
- Main.NoValueOptionHandler - Class in etomica.graph.view.rasterizer
-
Base class for options with no option value (i.e., the presence
of the option means something in itself.
- Main.OptionHandler - Interface in etomica.graph.view.rasterizer
-
Interface for handling one command line option
- Main.RectangleOptionHandler - Class in etomica.graph.view.rasterizer
-
Base class for options which expect a Rectangle optionValue.
- Main.SingleValueOptionHandler - Class in etomica.graph.view.rasterizer
-
Base class for options with a single option value.
- Main.TimeOptionHandler - Class in etomica.graph.view.rasterizer
-
Base class for options which expect the single optionValue to
be a time value.
- main1(String[]) - Static method in class etomica.models.co2.P2CO2Hellmann
-
- main1(String[]) - Static method in class etomica.models.water.P2WaterSzalewicz
-
- main2(String[]) - Static method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- main2(String[]) - Static method in class etomica.models.co2.P2CO2H2OWheatley
-
- main2(String[]) - Static method in class etomica.models.co2.PNCO2GCPM
-
- main2(String[]) - Static method in class etomica.models.co2.PNGCPM
-
- main2(String[]) - Static method in class etomica.models.water.P2WaterSzalewicz
-
- main2DGrid(String[]) - Static method in class etomica.models.co2.P2CO2H2OWheatley
-
Writes x-y grid of energies
- main3(String[]) - Static method in class etomica.models.water.P2WaterSzalewicz
-
- mainCO2(String[]) - Static method in class etomica.models.co2.PNGCPM
-
- mainQ(String[]) - Static method in class etomica.models.co2.P2CO2H2OWheatley
-
Check charges (all sums should be 0 for neutral molecules)
- mainTestU(String[]) - Static method in class etomica.models.co2.P2CO2H2OWheatley
-
Reads geometry.txt file and computes energy for each configuration
- makeAccumulator() - Method in interface etomica.modules.statistics.AccumulatorFactory
-
- makeAdjacentPairIterator() - Static method in class etomica.atom.iterator.ApiBuilder
-
Pair iterator that constructs pairs from the childlist atoms of a basis,
each with the atom adjacent to it in the list.
- makeAgent(IAtom, Box) - Method in class etomica.action.ActionMinimizeEnergy
-
- makeAgent(IAtom, Box) - Method in class etomica.association.AssociationManager
-
- makeAgent(IMolecule) - Method in class etomica.association.AssociationManagerMolecule
-
- makeAgent(IAtom, Box) - Method in class etomica.association.ColorSchemeSmer
-
- makeAgent(IAtom, Box) - Method in class etomica.association.MCMoveVolumeAssociated
-
- makeAgent(IMolecule) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- makeAgent(IAtom, Box) - Method in interface etomica.atom.AtomLeafAgentManager.AgentSource
-
Returns an agent for the given Atom.
- makeAgent(AtomType) - Method in interface etomica.atom.AtomTypeAgentManager.AgentSource
-
Returns an agent for the given AtomType.
- makeAgent(Box) - Method in interface etomica.box.BoxAgentManager.BoxAgentSource
-
- makeAgent(Box) - Method in class etomica.box.BoxAgentSourceAtomManager
-
- makeAgent(Box) - Method in class etomica.box.BoxAgentSourceMoleculeManager
-
- makeAgent(IAtom, Box) - Method in class etomica.conjugategradient.DerivativeEnergyFunction.MyAgentSource
-
- makeAgent(IAtom, Box) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG.MyAgentSource
-
- makeAgent(IMolecule) - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- makeAgent(IAtom, Box) - Method in class etomica.dimer.IntegratorDimerMin
-
- makeAgent(IAtom, Box) - Method in class etomica.dimer.IntegratorDimerRT
-
- makeAgent(IAtom, Box) - Method in class etomica.dimer.IntegratorEnergyMap
-
- makeAgent(IAtom, Box) - Method in class etomica.graphics.BondListener
-
- makeAgent(IAtom, Box) - Method in class etomica.graphics.ColorSchemeCollectiveAgent
-
- makeAgent(IAtom, Box) - Method in class etomica.graphics.ColorSchemeRandom
-
- makeAgent(IMolecule) - Method in class etomica.graphics.ColorSchemeRandomByMolecule
-
- makeAgent(IAtom, Box) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
AgentSource methods
- makeAgent(IAtom, Box) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedAgentSource
-
- makeAgent(IAtom, Box) - Method in class etomica.integrator.IntegratorConNVT
-
- makeAgent(IAtom, Box) - Method in class etomica.integrator.IntegratorGear4
-
- makeAgent(IAtom, Box) - Method in class etomica.integrator.IntegratorHard
-
Produces the Agent for this integrator.
- makeAgent(IAtom, Box) - Method in class etomica.integrator.IntegratorMD.VectorSource
-
- makeAgent(IMolecule) - Method in class etomica.integrator.IntegratorRigidIterative
-
- makeAgent(IAtom, Box) - Method in class etomica.integrator.IntegratorRigidIterative
-
- makeAgent(ISpecies) - Method in class etomica.integrator.IntegratorRigidIterative
-
- makeAgent(IMolecule) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- makeAgent(IAtom, Box) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- makeAgent(ISpecies) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- makeAgent(IAtom, Box) - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- makeAgent(IAtom, Box) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- makeAgent(ISpecies) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- makeAgent(IAtom, Box) - Method in class etomica.integrator.IntegratorVerlet
-
- makeAgent(IAtom, Box) - Method in class etomica.mappedvirial.MeterMappedU
-
- makeAgent(IAtom, Box) - Method in class etomica.mappedvirial.MeterMappedVirial
-
- makeAgent(IAtom, Box) - Method in class etomica.mappedvirial.MeterMappedVirialV
-
- makeAgent(IAtom, Box) - Method in class etomica.mappedvirial.MeterMeanForce
-
- makeAgent(IAtom, Box) - Method in class etomica.math.numerical.CalcGradientDifferentiable
-
- makeAgent(IAtom, Box) - Method in class etomica.models.clathrates.MinimizationTIP4P.ChargeAgentSourceRPM
-
- makeAgent(IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen.OrientationAgentSource
-
- makeAgent(IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource
-
- makeAgent(IAtom, Box) - Method in class etomica.models.water.ChargeAgentSourceTIP4PWater
-
- makeAgent(IAtom, Box) - Method in class etomica.modules.catalysis.InteractionTracker
-
- makeAgent(IAtom, Box) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- makeAgent(IAtom, Box) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
Implementation of AtomAgentManager.AgentSource interface.
- makeAgent(IAtom, Box) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- makeAgent(AtomType) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
-
- makeAgent(IAtom, Box) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
Implementation of AtomAgentManager.AgentSource interface.
- makeAgent(IAtom, Box) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- makeAgent(Box) - Method in class etomica.modules.colloid.NeighborListManagerColloid.NeighborListAgentSourceColloid
-
- makeAgent(IAtom, Box) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- makeAgent(IAtom, Box) - Method in class etomica.modules.droplet.IntegratorDroplet
-
- makeAgent(IAtom, Box) - Method in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
Implementation of Atom.AgentSource interface.
- makeAgent(IMolecule) - Method in class etomica.modules.rosmosis.MeterFlux
-
- makeAgent(IAtom, Box) - Method in class etomica.modules.rosmosis.P1Tether
-
- makeAgent(IMolecule) - Method in class etomica.modules.sam.CriterionTether3
-
- makeAgent(IMolecule) - Method in interface etomica.molecule.MoleculeAgentManager.MoleculeAgentSource
-
Returns an agent for the given Atom.
- makeAgent(Box) - Method in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- makeAgent(Box) - Method in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- makeAgent(IMolecule) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Returns the cell containing the given atom.
- makeAgent(IAtom, Box) - Method in class etomica.nbr.cell.NeighborCellManager
-
Returns the cell containing the given atom.
- makeAgent(IAtom, Box) - Method in class etomica.nbr.CriterionPositionWall
-
- makeAgent(IAtom, Box) - Method in class etomica.nbr.CriterionSimple
-
- makeAgent(Box) - Method in class etomica.nbr.list.BoxAgentSourceCellManagerList
-
- makeAgent(Box) - Method in class etomica.nbr.list.molecule.BoxAgentSourceCellManagerListMolecular
-
- makeAgent(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
-
- makeAgent(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- makeAgent(IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource
-
- makeAgent(Box) - Method in class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular.NeighborListSlantyAgentSourceMolecular
-
- makeAgent(Box) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- makeAgent(IAtom, Box) - Method in class etomica.nbr.list.NeighborCellManagerList
-
- makeAgent(IAtom, Box) - Method in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
-
- makeAgent(IAtom, Box) - Method in class etomica.nbr.list.NeighborListManager
-
- makeAgent(Box) - Method in class etomica.nbr.list.NeighborListManagerSlanty.NeighborListSlantyAgentSource
-
- makeAgent(Box) - Method in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- makeAgent(IMolecule) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- makeAgent(IAtom, Box) - Method in class etomica.nbr.site.NeighborSiteManager
-
- makeAgent(IAtom, Box) - Method in class etomica.normalmode.CoordinateDefinition.SiteSource
-
- makeAgent(IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource
-
- makeAgent(IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
-
- makeAgent(IAtom, Box) - Method in class etomica.normalmode.HSNPT.ActionSummer
-
- makeAgent(IAtom, Box) - Method in class etomica.normalmode.MeterDADB
-
- makeAgent(IAtom, Box) - Method in class etomica.normalmode.MeterSolidProps
-
- makeAgent(IAtom, Box) - Method in class etomica.normalmode.MeterSolidPropsLJ
-
- makeAgent(IAtom, Box) - Method in class etomica.paracetamol.ChargeAgentSourceParacetamol
-
- makeAgent(IMolecule) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol.OrientationAgentSource
-
- makeAgent(IAtom, Box) - Method in class etomica.potential.P2HardBondedList
-
- makeAgent(Box) - Method in class etomica.potential.P2SquareWellRobust
-
- makeAgent(IAtom, Box) - Method in class etomica.potential.P2SquareWellRobust
-
- makeAgent(AtomType) - Method in class etomica.potential.PotentialMasterMonatomic
-
- makeAgent(IMolecule) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- makeAgent(IAtom, Box) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- makeAgent(ISpecies) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- makeAgent(ISpecies) - Method in interface etomica.species.SpeciesAgentManager.AgentSource
-
Returns an agent for the given AtomType.
- makeAgent(IAtom, Box) - Method in class etomica.surfacetension.SurfaceTensionMapped
-
- makeAgent(Box) - Method in class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
-
- makeAgent(Box) - Method in class etomica.threaded.domain.PotentialMasterListThreaded.NeighborListAgentSourceThreaded
-
- makeAgent(IAtom, Box) - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- makeAndDisplayFrame(JPanel, String) - Static method in class etomica.graphics.SimulationGraphic
-
- makeAndDisplayFrame(JPanel) - Static method in class etomica.graphics.SimulationGraphic
-
- makeAndDisplayFrame() - Method in class etomica.graphics.SimulationGraphic
-
- makeAndDisplayFrame(String) - Method in class etomica.graphics.SimulationGraphic
-
- makeArrayD(int) - Method in class etomica.space.Space
-
- makeArrayD(double) - Method in class etomica.space.Space
-
- makeArrayD(int) - Method in class etomica.space1d.Space1D
-
- makeArrayD(double) - Method in class etomica.space1d.Space1D
-
- makeArrayD(int) - Method in class etomica.space2d.Space2D
-
- makeArrayD(double) - Method in class etomica.space2d.Space2D
-
- makeArrayD(int) - Method in class etomica.space3d.Space3D
-
- makeArrayD(double) - Method in class etomica.space3d.Space3D
-
- makeAtomTypes(IElement[]) - Static method in class etomica.species.SpeciesSpheresHetero
-
- makeAxilrodTeller() - Method in class etomica.models.co2.PNCO2GCPM
-
- makeAxilrodTeller() - Method in class etomica.models.co2.PNGCPM
-
- makeBigValue(double) - Method in class etomica.veos.Ushcats
-
- makeBigValue(IBigValue) - Method in class etomica.veos.Ushcats
-
- makeBond(IAtomList, Object) - Method in interface etomica.graphics.BondManager
-
Creates a bond object for the given pair with type determined by the
bondType object.
- makeBond(IAtomList, Object) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Add a bond to the graphical display between the given pairs.
- makeBox(Space, ClusterWeight) - Method in class etomica.virial.simulations.SimulationVirialOverlap2.BoxClusterFactory
-
- makeCachedPairPolarization() - Method in class etomica.models.co2.PNGCPM
-
- makeCachedPairPolarization() - Method in class etomica.models.water.PNWaterGCPM
-
- makeCopy() - Method in interface etomica.virial.ClusterAbstract
-
Returns another instance of an identical cluster (shallow copy).
- makeCopy() - Method in class etomica.virial.ClusterChainHS
-
- makeCopy() - Method in class etomica.virial.ClusterChainSoft
-
- makeCopy() - Method in class etomica.virial.ClusterCoupledAtomFlipped
-
- makeCopy() - Method in class etomica.virial.ClusterCoupledFlipped
-
- makeCopy() - Method in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- makeCopy() - Method in class etomica.virial.ClusterCoupledFlippedPartial
-
- makeCopy() - Method in class etomica.virial.ClusterDifference
-
- makeCopy() - Method in class etomica.virial.ClusterExchange
-
- makeCopy() - Method in class etomica.virial.ClusterMultiToSingle
-
- makeCopy() - Method in class etomica.virial.ClusterSinglyConnected
-
- makeCopy() - Method in class etomica.virial.ClusterSum
-
- makeCopy() - Method in class etomica.virial.ClusterSumAssociation
-
- makeCopy() - Method in class etomica.virial.ClusterSumEF
-
- makeCopy() - Method in class etomica.virial.ClusterSumHS
-
- makeCopy() - Method in class etomica.virial.ClusterSumIC
-
- makeCopy() - Method in class etomica.virial.ClusterSumMultibody
-
- makeCopy() - Method in class etomica.virial.ClusterSumMultibodyShell
-
- makeCopy() - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- makeCopy() - Method in class etomica.virial.ClusterSumPolarizable
-
- makeCopy() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- makeCopy() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- makeCopy() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- makeCopy() - Method in class etomica.virial.ClusterSumShell
-
- makeCopy() - Method in class etomica.virial.ClusterTree
-
- makeCopy() - Method in class etomica.virial.ClusterTreeEF
-
- makeCopy() - Method in class etomica.virial.ClusterWeightAbs
-
- makeCopy() - Method in class etomica.virial.ClusterWeightSumWall
-
- makeCopy() - Method in class etomica.virial.ClusterWeightUmbrella
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleyHS
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleyMultibody
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleyMultibodyBD
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleyMultibodyMix
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleySoft
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleySoftBD
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleySoftBDMix
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- makeCopy() - Method in class etomica.virial.ClusterWheatleySoftMix
-
- makeCopy() - Method in class etomica.virial.simulations.VirialH2OGCPMD.Clusterfoo
-
- makeData() - Method in interface etomica.data.IDataInfo
-
Returns a Data object appropriate for this DataInfo instance.
- makeData() - Method in class etomica.data.types.DataDouble.DataInfoDouble
-
- makeData() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArray
-
- makeData() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
-
- makeData() - Method in class etomica.data.types.DataFunction.DataInfoFunction
-
- makeData() - Method in class etomica.data.types.DataGroup.DataInfoGroup
-
- makeData() - Method in class etomica.data.types.DataTable.DataInfoTable
-
- makeData(int, int) - Static method in class etomica.data.types.DataTable
-
- makeData() - Method in class etomica.data.types.DataTensor.DataInfoTensor
-
- makeData() - Method in class etomica.data.types.DataVector.DataInfoVector
-
- MakeData - Class in etomica.models.oneDHardRods
-
- MakeData(int, double) - Constructor for class etomica.models.oneDHardRods.MakeData
-
- makeData(int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- makeDataInfo() - Method in class etomica.data.DataInfoFactory
-
Creates a new DataInfo object using the information held by this factory.
- makeDataInfo() - Method in interface etomica.data.IDataInfoFactory
-
Creates a new DataInfo object using the information held by this factory.
- makeDataInfo() - Method in class etomica.data.types.DataDouble.DataInfoDoubleFactory
-
- makeDataInfo() - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory
-
- makeDataInfo() - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
-
- makeDataInfo() - Method in class etomica.data.types.DataFunction.DataInfoFunctionFactory
-
- makeDataInfo() - Method in class etomica.data.types.DataGroup.DataInfoGroupFactory
-
- makeDataInfo() - Method in class etomica.data.types.DataTable.DataInfoTableFactory
-
- makeDataInfo() - Method in class etomica.data.types.DataTensor.DataInfoTensorFactory
-
- makeDataInfo() - Method in class etomica.data.types.DataVector.DataInfoVectorFactory
-
- makeDataProcessor() - Method in interface etomica.modules.statistics.AccumulatorFactory
-
- makeDataSink() - Method in class etomica.data.DataSet
-
- makeDataSink(IDataInfo) - Method in class etomica.data.DataSinkTable
-
- makeDataSink(int) - Method in interface etomica.data.DataSplitter.IDataSinkFactory
-
- makeDipole() - Static method in class etomica.rotation.SingleDipole
-
- makeDropShape() - Method in class etomica.modules.droplet.DropletAtomic
-
- makeDWPlot - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- makeF(Potential2Spherical, double) - Static method in class etomica.virial.CalcFFT
-
- makeFccVectors(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- makeFullStar() - Method in class etomica.virial.cluster.ClusterDiagram
-
Turns this cluster into a full star -- each point in the cluster is
connected to every other point in the cluster.
- makeGraph(long) - Static method in class etomica.graph.util.GraphNumber
-
- makeGraph(long, byte) - Static method in class etomica.graph.util.GraphNumber
-
- makeGraphicsPanel() - Method in class etomica.modules.clustergenerator.MyApplet
-
- makeGraphList() - Static method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- makeGraphList() - Static method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- makeGraphList() - Static method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- makeGraphList() - Static method in class etomica.virial.cluster.VirialDiagrams
-
- makeGraphList() - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- makeGraphList() - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- makeGraphList() - Static method in class etomica.virial.cluster.VirialDiagramsPT
-
- makeGraphList() - Static method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- makeGraphList() - Static method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- makeHcpVectors(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- makeHistogram() - Method in interface etomica.data.AccumulatorAverageBootstrap.HistogramFactory
-
- makeHistoryPlot(ArrayList<DataPump>, DataSourceCountSteps, JPanel, DataPumpListener, String) - Method in class etomica.modules.statistics.StatisticsMCGraphic
-
- makeInputFile(Vector, Vector) - Method in class etomica.potential.P2QChem
-
- makeInputFile(IMoleculeList) - Method in class etomica.potential.PotentialEmul
-
- makeIntegratorListener(PotentialMaster, Box) - Method in class etomica.meam.P2EAM
-
Creates and returns an integrator listener that makes the integrator's
force sum work properly by running an energy calculation first.
- makeIntergroupTypeIterator(AtomType[]) - Static method in class etomica.atom.iterator.ApiBuilder
-
Returns an intergroup iterator that filters the iterates so that only
those having the given type instances are returned.
- makeInterspeciesPairIterator(ISpecies[]) - Method in class etomica.molecule.iterator.IteratorFactory
-
creates a pair iterator which loops over all pairs in a neighbor list
between two groups
- makeIntraspeciesPairIterator(ISpecies) - Method in class etomica.molecule.iterator.IteratorFactory
-
creates a pair iterator which loops over all pairs in a neighbor list
within one group
- makeLeafAtom(AtomType) - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- makeLeafAtom(AtomType) - Method in class etomica.paracetamol.SpeciesParacetamol
-
- makeLeafAtom() - Method in class etomica.species.SpeciesPolyhedron
-
- makeLeafAtom() - Method in class etomica.species.SpeciesSpheres
-
- makeLeafAtom(AtomType) - Method in class etomica.species.SpeciesSpheresHetero
-
- makeLeafAtom() - Method in class etomica.species.SpeciesSpheresMono
-
- makeLeafAtom() - Method in class etomica.species.SpeciesSpheresRotating
-
- makeLeafAtom() - Method in class etomica.species.SpeciesSpheresRotatingMolecule
-
- makeLrc - Variable in class etomica.potential.P2SoftSphericalTruncated
-
- makeLrcPotential(AtomType[]) - Method in class etomica.potential.P2SoftSphericalTruncated
-
Returns the zero-body potential that evaluates the contribution to the
energy and its derivatives from pairs that are separated by a distance
exceeding the truncation radius.
- makeLrcPotential(AtomType[]) - Method in class etomica.potential.P2SoftSphericalTruncatedShifted
-
Returns null because the shift can't be corrected.
- makeLrcPotential(AtomType[]) - Method in class etomica.potential.P2SoftTruncated
-
Returns the zero-body potential that evaluates the contribution to the
energy and its derivatives from pairs that are separated by a distance
exceeding the truncation radius.
- makeLrcPotential(AtomType[]) - Method in interface etomica.potential.PotentialTruncated
-
Returns a class that calculates the long-range contribution to the potential
that becomes neglected by the truncation.
- makeMCMoveListener() - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- makeMCMoveListener() - Method in class etomica.nbr.cell.NeighborCellManager
-
- makeMCMoveSwap(IntegratorBox, IntegratorBox, Space) - Method in interface etomica.integrator.IntegratorPT.MCMoveSwapFactory
-
- makeMCMoveSwap(IntegratorBox, IntegratorBox, Space) - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration.SwapFactory
-
- makeMCMoveSwap(IntegratorBox, IntegratorBox, Space) - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster.SwapFactory
-
- makeMolecule() - Method in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- makeMolecule() - Method in class etomica.AlkaneEH.SpeciesMethane
-
- makeMolecule() - Method in class etomica.models.nitrogen.SpeciesN2
-
- makeMolecule() - Method in class etomica.models.nitrogen.SpeciesN2B
-
- makeMolecule() - Method in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- makeMolecule() - Method in class etomica.models.OPLS.SpeciesAceticAcid
-
- makeMolecule() - Method in class etomica.models.rowley.SpeciesEthanol
-
- makeMolecule() - Method in class etomica.models.rowley.SpeciesMethanol
-
- makeMolecule() - Method in class etomica.models.traPPE.SpeciesMethanol
-
- makeMolecule() - Method in class etomica.models.water.SpeciesWater3P
-
- makeMolecule() - Method in class etomica.models.water.SpeciesWater3POriented
-
- makeMolecule() - Method in class etomica.models.water.SpeciesWater4P
-
- makeMolecule() - Method in class etomica.models.water.SpeciesWater4PCOM
-
- makeMolecule() - Method in class etomica.models.water.SpeciesWater4POriented
-
- makeMolecule() - Method in class etomica.normalmode.SpeciesHSDimer
-
- makeMolecule() - Method in class etomica.paracetamol.SpeciesParacetamol
-
- makeMolecule() - Method in interface etomica.species.ISpecies
-
Builds and returns the IMolecule of this ISpecies.
- makeMolecule() - Method in class etomica.species.SpeciesSpheres
-
Constructs a new group.
- makeMolecule() - Method in class etomica.species.SpeciesSpheresCustom
-
Constructs a new group containing a block of atoms for
each sub-type.
- makeMolecule() - Method in class etomica.species.SpeciesSpheresHetero
-
Constructs a new group containing a block of atoms for
each sub-type.
- makeMolecule() - Method in class etomica.species.SpeciesSpheresMono
-
Constructs a new group.
- makeMolecule() - Method in class etomica.species.SpeciesSpheresRotatingMolecule
-
Constructs a new group.
- makeMolecule() - Method in class etomica.virial.Species7SiteRigidSF6
-
- makeMolecule() - Method in class etomica.virial.SpeciesAlkane
-
- makeMolecule() - Method in class etomica.virial.SpeciesAnthracene3site464
-
- makeMolecule() - Method in class etomica.virial.SpeciesAnthracene3site545
-
- makeMolecule() - Method in class etomica.virial.SpeciesMethane
-
- makeMolecule() - Method in class etomica.virial.SpeciesPh3site464
-
- makeMolecule() - Method in class etomica.virial.SpeciesPh3site545
-
- makeMolecule() - Method in class etomica.virial.SpeciesTraPPEAnthracene
-
- makeMolecule() - Method in class etomica.virial.SpeciesTraPPECO2
-
- makeMolecule() - Method in class etomica.virial.SpeciesTraPPENaphthalene
-
- makeMolecule() - Method in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- makeMoleculeIterator(ISpecies[]) - Method in class etomica.molecule.iterator.IteratorFactory
-
Selects an appropriate iterator for the given species array.
- makeMuHistoryPlot(ArrayList<DataPump>, DataSourceCountSteps, JPanel, DataPumpListener, String) - Method in class etomica.modules.statistics.StatisticsMCGraphic
-
- makeNB(int) - Method in class etomica.virial.PotentialNonAdditive
-
- makeNominalMoment(Space) - Static method in class etomica.species.SpeciesSpheresRotatingMolecule
-
- makeNonAdjacentPairIterator() - Static method in class etomica.atom.iterator.ApiBuilder
-
Pair iterator that constructs pairs from the childlist atoms of a basis,
each with all atoms that are not adjacent to it in the list.
- makeNonAdjacentPairIterator(int) - Static method in class etomica.atom.iterator.ApiBuilder
-
- makeOrientation() - Method in class etomica.space.Space
-
- makeOrientation() - Method in class etomica.space1d.Space1D
-
- makeOrientation() - Method in class etomica.space2d.Space2D
-
- makeOrientation() - Method in class etomica.space3d.Space3D
-
- makeP0() - Method in class etomica.potential.P2ReactionFieldDipole
-
- makeP0() - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
Returns a 0-body potential that should be added along with this
potential.
- makeP1IntraSimple(PotentialMaster, Potential2, Potential2) - Static method in class etomica.potential.P1IntraSimple
-
- makeP2EwaldReal() - Method in class etomica.potential.EwaldSummation
-
- makePairPotentialsUnlike(int, int) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- makeParameters(char[], byte) - Static method in class etomica.graph.operations.MulFlexible.MulFlexibleParameters
-
Parameters that specify that the resulting product should include graphs
containing up to nFieldNodes field nodes and that nodes of a color
included in flexColors never be superimposed unless one of the nodes is
unbonded.
- makeParametersOnlyRootPt(char[], byte) - Static method in class etomica.graph.operations.MulFlexible.MulFlexibleParameters
-
- makeParametersWithNodes(char[], byte, byte, byte) - Static method in class etomica.graph.operations.MulFlexible.MulFlexibleParameters
-
Parameters that specify that the resulting product should include graphs
containing up to nFieldNodes field nodes and that node1ID from the first
graph and node2ID from the second graph should be superimposed (if
possible).
- makePotentialGroup(int) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- makePotentialGroup(int) - Method in class etomica.nbr.PotentialMasterHybrid
-
- makePotentialGroup(int) - Method in class etomica.nbr.PotentialMasterNbr
-
- makePotentialGroup(int) - Method in class etomica.potential.PotentialMaster
-
Returns an nBody PotentialGroup appropriate for this type of
PotentialMaster.
- makeQFH(double) - Method in class etomica.potential.P2HePCKLJS
-
- makeQFH(double) - Method in class etomica.potential.P2HeSimplified
-
- makeQFH(double) - Method in class etomica.potential.P2NitrogenHellmann
-
- makeReciprocal() - Method in class etomica.lattice.crystal.Primitive
-
Method defining and constructing reciprocal primitive;
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveBcc
-
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveCubic
-
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveFcc
-
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveGeneral
-
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- makeReciprocal() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- makeReciprocal() - Method in class etomica.models.hexane.PrimitiveHexane
-
- makeReeHoover(ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations
-
Creates a set of Ree-Hoover clusters from the given cluster.
- makeReeHoover(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
- makeReferenceF(Space, int, double[][]) - Static method in class etomica.virial.MayerHSMixture
-
- makeRhoCluster(MayerFunction, boolean) - Method in class etomica.virial.cluster.ExternalVirialDiagrams
-
- makeRhoDiagrams() - Method in class etomica.virial.cluster.ExternalVirialDiagrams
-
- makeRhoDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- makeRhoDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- makeRhoDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- makeRhoDiagrams() - Method in class etomica.virial.cluster.VirialDiagrams
-
- makeRhoDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- makeRhoDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- makeRhoDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- makeRhoDiagrams() - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- makeRhoDiagrams() - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- makeRotationTensor() - Method in class etomica.space.Space
-
- makeRotationTensor() - Method in class etomica.space1d.Space1D
-
- makeRotationTensor() - Method in class etomica.space2d.Space2D
-
- makeRotationTensor() - Method in class etomica.space3d.Space3D
-
- makeScaledCoordinates(Space, Basis, int[]) - Static method in class etomica.normalmode.BasisBigCell
-
- makeSemiclassical(double) - Method in class etomica.models.co2.P2CO2H2OWheatley
-
Creates a Feynman-Hibbs implementation of a semi-classical potential based on this model for the given temperature.
- makeSemiclassical(double) - Method in class etomica.models.co2.P2CO2Hellmann
-
- makeSemiclassical(double) - Method in class etomica.models.water.P2WaterSzalewicz
-
- makeSemiclassicalTI(double) - Method in class etomica.models.co2.P2CO2H2OWheatley
-
Creates a Takahashi-Imada implementation of a semi-classical potential based on this model for the given temperature.
- makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.VirialDiagrams
-
- makeSingleVirialClusters(ClusterSum, MayerFunction[][], int, int[]) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction[], int) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- makeSingleVirialClusters(ClusterSum, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- makeSingleVirialClustersMulti(ClusterSumMultibody, MayerFunction, MayerFunctionNonAdditive) - Method in class etomica.virial.cluster.VirialDiagrams
-
- makeSingleWater() - Static method in class etomica.rotation.SingleDumbellRattle
-
- makeSingleWater() - Static method in class etomica.rotation.SingleDumbellShake
-
- makeSingleWater() - Static method in class etomica.rotation.SingleWater
-
- makeSingleWater() - Static method in class etomica.rotation.SingleWaterMatrix
-
- makeSingleWater() - Static method in class etomica.rotation.SingleWaterRattle
-
- makeSingleWater() - Static method in class etomica.rotation.SingleWaterShake
-
- makeSite(AbstractLattice, int[]) - Method in interface etomica.lattice.SiteFactory
-
Constructs a site for placement in a lattice.
- makeSite(AbstractLattice, int[]) - Method in class etomica.nbr.cell.Cell.CellFactory
-
- makeSite(AbstractLattice, int[]) - Method in class etomica.nbr.cell.molecule.CellMolecular.CellFactory
-
- makeSpecies(Simulation) - Method in class etomica.chem.models.Model
-
Creates a species in the given simulation and returns it.
- makeSpecies(Space) - Method in class etomica.models.rowley.SpeciesFactoryEthanol
-
- makeSpecies(Space) - Method in class etomica.models.rowley.SpeciesFactoryMethanol
-
- makeSpecies(Space) - Method in class etomica.models.traPPE.SpeciesFactoryMethanol
-
- makeSpecies(Space) - Method in interface etomica.virial.SpeciesFactory
-
- makeSpecies(Space) - Method in class etomica.virial.SpeciesFactoryOrientedSpheres
-
- makeSpecies(Space) - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- makeSpecies(Space) - Method in class etomica.virial.SpeciesFactorySpheres
-
- makeSpecies(Space) - Method in class etomica.virial.SpeciesFactorySpheres2
-
- makeSpecies(Space) - Method in class etomica.virial.SpeciesFactoryTangentSpheres
-
- makeSpecies(Space) - Method in class etomica.virial.SpeciesFactoryWater3P
-
- makeSpecies(Space) - Method in class etomica.virial.SpeciesFactoryWater4P
-
- makeSpecies(Space) - Method in class etomica.virial.SpeciesFactoryWaterGCPM
-
- makeSpeciesInternal(Simulation) - Method in class etomica.chem.models.Model
-
Internal method to be implemented by subclasses to create the actual
Species object for the given Simulation.
- makeSpeciesInternal(Simulation) - Method in class etomica.chem.models.ModelChain
-
- makeStuff(String, ParserLAMMPS.Options) - Static method in class etomica.parser.ParserLAMMPS
-
- makeStuffFromLines(List<String>, ParserLAMMPS.Options) - Static method in class etomica.parser.ParserLAMMPS
-
- makeTargetF(int, double[][]) - Static method in class etomica.virial.MayerHSMixture
-
- makeTensor() - Method in class etomica.space.Space
-
- makeTensor() - Method in class etomica.space1d.Space1D
-
- makeTensor() - Method in class etomica.space2d.Space2D
-
- makeTensor() - Method in class etomica.space3d.Space3D
-
- makeTerminalSink() - Method in class etomica.data.DataArrayWriter
-
- makeTerminalSink() - Method in class etomica.data.DataTableWriter
-
- makeTI(double) - Method in class etomica.potential.P2HePCKLJS
-
- makeTI(double) - Method in class etomica.potential.P2HeSimplified
-
- makeTI(double) - Method in class etomica.potential.P2O2Bartolomei
-
- makeUniqueElementSymbol(String) - Method in class etomica.simulation.Simulation
-
Method to allow generation of unique string to identify Elements in the Simulation.
- makeVector() - Method in class etomica.space.Space
-
- makeVector(int) - Static method in class etomica.space.Space
-
Returns a Vector from the space of the given dimension.
- makeVector(double...) - Static method in class etomica.space.Space
-
- makeVector(int...) - Static method in class etomica.space.Space
-
- makeVector() - Method in class etomica.space1d.Space1D
-
- makeVector() - Method in class etomica.space2d.Space2D
-
- makeVector() - Method in class etomica.space3d.Space3D
-
- makeVectorArray(int) - Method in class etomica.space.Space
-
Makes an array of Vectors.
- makeVirialCluster(MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- makeVirialCluster(MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- makeVirialCluster(MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- makeVirialCluster(MayerFunction) - Method in class etomica.virial.cluster.VirialDiagrams
-
- makeVirialCluster(MayerFunction, MayerFunctionNonAdditive) - Method in class etomica.virial.cluster.VirialDiagrams
-
- makeVirialCluster(MayerFunction, MayerFunctionNonAdditive, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- makeVirialCluster(Set<Graph>, MayerFunction, MayerFunctionNonAdditive) - Method in class etomica.virial.cluster.VirialDiagrams
-
- makeVirialCluster(MayerFunction[][], int, int[]) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- makeVirialCluster(Set<Graph>, MayerFunction[][], int, int[]) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- makeVirialCluster(MayerFunction, MayerFunction[]) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- makeVirialCluster(Set<Graph>, MayerFunction, MayerFunction[]) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- makeVirialCluster(MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- makeVirialClusterHS(Set<Graph>, MayerFunction) - Method in class etomica.virial.cluster.VirialDiagrams
-
- makeVirialClusterSecondTemperatureDerivative(MayerFunction, MayerFunction, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.VirialDiagrams
-
- makeVirialClusterTempDeriv(MayerFunction, MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.VirialDiagrams
-
- makeVirialDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- makeVirialDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- makeVirialDiagrams() - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- makeVirialDiagrams() - Method in class etomica.virial.cluster.VirialDiagrams
-
- makeVirialDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- makeVirialDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- makeVirialDiagrams() - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- makeVirialDiagrams() - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- makeWaterBox() - Static method in class etomica.rotation.WaterBox
-
- makeWaterDroplet() - Static method in class etomica.rotation.WaterDroplet
-
- makeWaterDroplet() - Static method in class etomica.rotation.WaterDropletMatrix
-
- makeWaterDroplet() - Static method in class etomica.rotation.WaterDropletRattle
-
- makeWaterDroplet() - Static method in class etomica.rotation.WaterDropletShake
-
- makeWaterDroplet() - Static method in class etomica.rotation.WaterTrimer
-
- makeWaterDroplet() - Static method in class etomica.rotation.WaterTrimerRattle
-
- makeWaterDroplet() - Static method in class etomica.rotation.WaterTrimerShake
-
- makeWaveVector(double) - Method in class etomica.data.meter.MeterStructureFactor
-
- makeWaveVectors(Box) - Method in interface etomica.normalmode.WaveVectorFactory
-
Tells the instance to make wave vectors appropriate for the given box.
- makeWaveVectors(Box) - Method in class etomica.normalmode.WaveVectorFactory1D
-
- makeWaveVectors(Box) - Method in class etomica.normalmode.WaveVectorFactory2D
-
- makeWaveVectors(Box) - Method in class etomica.normalmode.WaveVectorFactoryFcc
-
- makeWaveVectors(Box) - Method in class etomica.normalmode.WaveVectorFactoryFromFile
-
- makeWaveVectors(Box) - Method in class etomica.normalmode.WaveVectorFactorySimple
-
- makeWaveVectors(Box) - Method in class etomica.normalmode.WaveVectorFactorySuperBox
-
- makeWeightCluster(ClusterAbstract[]) - Method in interface etomica.virial.ClusterWeight.Factory
-
- makeWeightCluster(ClusterAbstract) - Static method in class etomica.virial.ClusterWeightAbs
-
- makeWeightClusters(ClusterAbstract[]) - Static method in class etomica.virial.ClusterWeightAbs
-
- makeWertheimCluster(MayerFunction, MayerFunction) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- makeWertheimDiagrams() - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- makeWrapper(Object) - Method in class etomica.meta.SimulationModel
-
Ensures that a wrapper is defined for the given object and, recursively, all other objects referenced by it.
- makeWrapperObject(Class) - Method in class etomica.util.ReadParameters
-
- makeX() - Method in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- manager - Variable in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
-
- managerPanel - Variable in class etomica.modules.clustergenerator.MyApplet
-
- map(IFunction) - Method in interface etomica.data.IData
-
Maps the function on all data values, replace each with the value given
by the function applied to it.
- map(IFunction) - Method in class etomica.data.types.DataDouble
-
Maps the function on this instance's value, replacing it with the value
returned by the function.
- map(IFunction) - Method in class etomica.data.types.DataDoubleArray
-
Replaces all values by the value of the function applied to each.
- map(IFunction) - Method in class etomica.data.types.DataDoubleBDArray
-
Replaces all values by the value of the function applied to each.
- map(IFunction) - Method in class etomica.data.types.DataGroup
-
- map(IFunction) - Method in class etomica.data.types.DataTensor
-
Maps the function on all vector elements, replacing each with the value
given by the function applied to it.
- map(IFunction) - Method in class etomica.data.types.DataVector
-
Maps the function on all vector elements, replacing each with the
value given by the function applied to it.
- map(byte) - Method in class etomica.graph.operations.RelabelParameters
-
- map(IFunction) - Method in interface etomica.space.Tensor
-
Applies given function to each element of this tensor.
- map(IFunction) - Method in interface etomica.space.Vector
-
Applies the given function to each element of the vector.
- map(IFunction) - Method in class etomica.space1d.Tensor1D
-
- map(IFunction) - Method in class etomica.space1d.Vector1D
-
- map(IFunction) - Method in class etomica.space2d.Tensor2D
-
- map(IFunction) - Method in class etomica.space2d.Vector2D
-
- map(IFunction) - Method in class etomica.space3d.Tensor3D
-
- map(IFunction) - Method in class etomica.space3d.Vector3D
-
- map(IFunction) - Method in class etomica.spaceNd.TensorND
-
- map(IFunction) - Method in class etomica.spaceNd.VectorND
-
- MappedRdf - Class in etomica.mappedRdf
-
Created by aksharag on 5/15/17.
- MappedRdf(Space, int, double, double, double) - Constructor for class etomica.mappedRdf.MappedRdf
-
- MappedRdf.LJMDParams - Class in etomica.mappedRdf
-
- MappedU - Class in etomica.mappedvirial
-
- MappedU(Space, int, double, double, double) - Constructor for class etomica.mappedvirial.MappedU
-
- MappedU.LJMDParams - Class in etomica.mappedvirial
-
- MappedVirialLJ - Class in etomica.mappedvirial
-
- MappedVirialLJ(Space, int, double, double, double) - Constructor for class etomica.mappedvirial.MappedVirialLJ
-
- MappedVirialLJ.LJMDParams - Class in etomica.mappedvirial
-
- MappedVirialLJVGr - Class in etomica.mappedvirial
-
- MappedVirialLJVGr(Space, int, double, double, double) - Constructor for class etomica.mappedvirial.MappedVirialLJVGr
-
- MappedVirialLJVGr.LJMDParams - Class in etomica.mappedvirial
-
- mapValue(String) - Method in class org.jmol.script.ScriptVariable
-
- markDirty() - Method in class etomica.math.numerical.AkimaSpline
-
- markLines(String, char) - Static method in class org.jmol.util.Parser
-
- MAROON - Static variable in class org.jmol.util.Colix
-
- maskSingleBit(int) - Method in class etomica.graph.model.impl.BitmapOfLong
-
Returns a long with a single bit set, corresponding to the bit offset of the given
bit index.
- maskSingleBit(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
Returns a long with a single bit set, corresponding to the bit offset of the given
bit index.
- maskSingleLong() - Method in class etomica.graph.model.impl.BitmapOfLong
-
Returns a bitmask corresponding to the valid bits of the long with the given index.
- maskSingleLong(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
Returns a bitmask corresponding to the valid bits of the long with the given index.
- mass - Variable in class etomica.chem.elements.ElementChemical
-
- mass - Variable in class etomica.chem.elements.ElementSimple
-
- mass - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- mass - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- mass - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- mass - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MassEditor
-
- mass - Variable in class etomica.modules.swmd.SwmdGraphic
-
- mass - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
-
- mass - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
-
- mass - Variable in class etomica.potential.P2HePCKLJS.P2HeQFH
-
- mass - Variable in class etomica.potential.P2HePCKLJS.P2HeTI
-
- mass - Variable in class etomica.potential.P2HeSimplified.P2HeQFH
-
- mass - Variable in class etomica.potential.P2HeSimplified.P2HeTI
-
- mass - Variable in class etomica.potential.P2O2Bartolomei.P2O2TI
-
- mass - Variable in class etomica.species.SpeciesOriented
-
- Mass - Class in etomica.units.dimensions
-
Dimension for all units of mass.
- mass() - Method in class etomica.units.systems.CGS
-
- mass - Variable in class etomica.units.systems.LJ
-
- mass() - Method in class etomica.units.systems.LJ
-
- mass() - Method in class etomica.units.systems.MKS
-
- mass() - Method in class etomica.units.systems.UnitSystem
-
- mass() - Method in class etomica.units.systems.UnitSystem.Sim
-
- mass - Static variable in class org.jmol.script.Token
-
- mass0 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- mass0 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- mass1 - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- massBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- massBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- massBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- massBox - Variable in class etomica.modules.swmd.SwmdGraphic
-
- MassEditor(SpeciesSpheresMono, String) - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MassEditor
-
- massH - Variable in class etomica.models.water.PNWaterGCPM
-
- massH - Static variable in class etomica.virial.simulations.VirialH2PISimple
-
- massMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- massN - Static variable in class etomica.virial.simulations.VirialN2
-
- massN - Static variable in class etomica.virial.simulations.VirialN2PI
-
- massN2 - Static variable in class etomica.potential.P2NitrogenHellmann
-
- massO - Variable in class etomica.models.water.PNWaterGCPM
-
- massO - Static variable in class etomica.virial.simulations.VirialO2PI
-
- MassProductionVirialRowleyAlcohol - Class in etomica.models.rowley
-
- MassProductionVirialRowleyAlcohol() - Constructor for class etomica.models.rowley.MassProductionVirialRowleyAlcohol
-
- massSolute - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- massSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- mat4 - Variable in class org.jmol.util.MeshSurface
-
- Match - Class in etomica.graph.isomorphism
-
- Match() - Constructor for class etomica.graph.isomorphism.Match
-
- match(Graph, Graph, boolean) - Static method in class etomica.graph.isomorphism.Match
-
Execution of an isomorphism test with the default algorithm.
- match(SearchState) - Static method in class etomica.graph.isomorphism.Match
-
Execution of an isomorphism test with a provided initial state.
- MaterialFracture - Class in etomica.modules.materialfracture
-
- MaterialFracture() - Constructor for class etomica.modules.materialfracture.MaterialFracture
-
- MaterialFractureGraphic - Class in etomica.modules.materialfracture
-
Graphical components for Material Fracture module
- MaterialFractureGraphic(MaterialFracture) - Constructor for class etomica.modules.materialfracture.MaterialFractureGraphic
-
- MaterialFractureGraphic.Applet - Class in etomica.modules.materialfracture
-
- matrix3f - Static variable in class org.jmol.script.Token
-
- Matrix3f - Class in org.jmol.util
-
A single precision floating point 3 by 3 matrix.
- Matrix3f() - Constructor for class org.jmol.util.Matrix3f
-
Constructs and initializes a Matrix3f to all zeros.
- matrix4f - Static variable in class org.jmol.script.Token
-
- Matrix4f - Class in org.jmol.util
-
A single precision floating point 4 by 4 matrix.
- Matrix4f() - Constructor for class org.jmol.util.Matrix4f
-
- MATRIX_A - Static variable in class etomica.util.random.RandomMersenneTwister
-
- matrixPermutation(int[], int[][]) - Static method in class etomica.math.discrete.PermutationIterator
-
Returns a new matrix formed by permuting the rows and columns of the
given matrix according to the permuation list p.
- matrixToScript(Object) - Static method in class org.jmol.util.Escape
-
- max - Variable in class etomica.lattice.IndexIteratorIncreasing
-
- max(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor
-
Maximum of two values.
- max(Vector<Ifactor>) - Static method in class etomica.veos.bigdecimal.Ifactor
-
Maximum of a list of values.
- max(Rational) - Method in class etomica.veos.bigdecimal.Rational
-
Compares the value of this with another constant.
- max - Static variable in class org.jmol.script.Token
-
- MAX_INT - Static variable in class etomica.veos.bigdecimal.Rational
-
The maximum and minimum value of a standard Java integer, 2^31.
- max_l - Variable in class etomica.potential.P2HydrogenPatkowski
-
- max_l - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- MAX_X - Static variable in class etomica.graphics.DevicePlotPoints
-
- MAX_Y - Static variable in class etomica.graphics.DevicePlotPoints
-
- maxAdjustInterval - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
-
- maxAngle - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- maxBias - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- maxBiasMinN - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- maxBiasR - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- maxBlocks - Variable in class etomica.data.AccumulatorAverageCollapsing
-
- maxBlockSize - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
-
- maxBlockSize - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- maxBlockSize - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
-
- maxBonds - Variable in class etomica.association.AssociationHelperBranched
-
- maxBonds - Variable in class etomica.association.AssociationHelperMolecule
-
- maxcf - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
-
- maxChainLength - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- maxChainLength - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- maxChainLength - Variable in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- maxCount - Variable in class etomica.graph.iterators.filters.FieldNodeCount
-
- maxCount - Variable in class etomica.graph.property.FieldNodeCountMax
-
- maxDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- maxDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- maxEta - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- maxExchangeNodes - Variable in class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
-
- maxFloat - Variable in class etomica.graphics.DisplayTable
-
- maxHeight - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Maximum output image height.
- maximum() - Method in class etomica.math.DoubleRange
-
The maximum defined by this range.
- MAXIMUM_AUTO_BOND_COUNT - Static variable in class org.jmol.viewer.JmolConstants
-
- MAXIMUM_QUALITY - Static variable in class etomica.graph.view.rasterizer.SVGConverter
-
Maximum quality value
- maxIndex() - Method in interface etomica.veos.BetaSource
-
Returns k such that beta[j] == 0 for all j > k.
- maxIndex() - Method in class etomica.veos.HardRods
-
- maxIndex() - Method in class etomica.veos.VanderWaals
-
- maxIndex - Variable in class etomica.virial.cluster.PermutationIterator
-
- maxInsertDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- maxInsertDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- MaxIsomorph - Class in etomica.graph.operations
-
Returns a set of graphs with each one corresponding to a graph in the
original set.
- MaxIsomorph() - Constructor for class etomica.graph.operations.MaxIsomorph
-
- maxIsomorph - Variable in class etomica.graph.property.FFTDecomposition
-
- maxIsomorph - Variable in class etomica.graph.property.IsFFT
-
- MaxIsomorph.MaxIsomorphParameters - Class in etomica.graph.operations
-
Parameters class for MaxIsomorph which defines a graph operation and
property to select for.
- MaxIsomorphCriteriaMixture() - Constructor for class etomica.virial.cluster.VirialDiagramsMix2.MaxIsomorphCriteriaMixture
-
- MaxIsomorphParameters(GraphOp, Property) - Constructor for class etomica.graph.operations.MaxIsomorph.MaxIsomorphParameters
-
- MaxIsomorphWertheim - Class in etomica.graph.operations
-
Returns a set of graphs with each one corresponding to a graph in the
original set.
- MaxIsomorphWertheim() - Constructor for class etomica.graph.operations.MaxIsomorphWertheim
-
- MaxIsomorphWertheim.MaxIsomorphWertheimParameters - Class in etomica.graph.operations
-
- MaxIsomorphWertheimParameters(CombineABSite.CombineABSiteParameters) - Constructor for class etomica.graph.operations.MaxIsomorphWertheim.MaxIsomorphWertheimParameters
-
- MaxIsomorphWertheimParameters(Property, CombineABSite.CombineABSiteParameters) - Constructor for class etomica.graph.operations.MaxIsomorphWertheim.MaxIsomorphWertheimParameters
-
- maxIterations - Variable in class etomica.integrator.IntegratorRigidIterative
-
- maxIterations - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- maxIterations - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- maxIterations - Variable in class etomica.modules.interfacial.FitTanh
-
- maxIterations - Variable in class etomica.surfacetension.FitTanh
-
- maxLength - Variable in class etomica.association.MCMoveAtomMonomer
-
- maxLength - Variable in class etomica.association.MCMoveAtomSmer
-
- maxLength - Variable in class etomica.association.MCMoveMoleculeMonomer
-
- maxLength - Variable in class etomica.association.MCMoveMoleculeRotateAssociated
-
- maxLength - Variable in class etomica.association.MCMoveMoleculeSmer
-
- maxLength - Variable in class etomica.association.MCMoveRotateAssociated
-
- maxLPN - Static variable in class etomica.math.SpecialFunctions
-
- maxMolecule - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- maxN - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- maxNbrsVapor - Variable in class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- maxNumAtoms - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- maxNumAtoms - Variable in class etomica.virial.PotentialEmulCached
-
- maxNumBeads - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- maxNumBlocks - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- maxpar1 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- maxpar2 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- maxPhi - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- maxRatio - Variable in class etomica.data.DataPumpListenerPow
-
- maxRunNumber - Variable in class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
-
- maxRunNumber - Variable in class etomica.virial.simulations.VirialSQWRecalcSmallMem.VirialHSParam
-
- maxSample - Variable in class etomica.data.AccumulatorAverageCollapsingLogAB
-
- maxSampleValue - Variable in class etomica.virial.MeterVirialBDBin
-
- maxSleep - Variable in class etomica.graphics.DeviceDelaySlider
-
- maxSphereCache - Static variable in class org.jmol.util.Shader
-
- maxSteps - Variable in class etomica.action.ActionIntegrate
-
- maxSteps - Variable in class etomica.action.ActionMinimizeEnergy
-
- maxSteps - Variable in class etomica.action.activity.ActivityIntegrate
-
- maxVacancy - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- MaxwellBoltzmann - Class in etomica.statmech
-
Non-instantiable class with static methods for implementing features of the
Maxwell-Boltzmann velocity distribution.
- MaxwellBoltzmann.Distribution - Class in etomica.statmech
-
Function giving the Maxwell-Boltzmann distribution of speeds.
- maxWidth - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Maximum output image width.
- maxwidth - Variable in class etomica.util.ScientificFormat
-
- maybeTrimToSize() - Method in class etomica.atom.AtomArrayList
-
- maybeTrimToSize() - Method in class etomica.molecule.MoleculeArrayList
-
- MayerD2FDT2Spherical - Class in etomica.virial
-
Required for computing second derivatives of virial coefficients w/r to temperature
- MayerD2FDT2Spherical(Potential2Spherical) - Constructor for class etomica.virial.MayerD2FDT2Spherical
-
Constructor for MayerESpherical.
- MayerDFDTSpherical - Class in etomica.virial
-
Required for computing temperature derivatives of virial coefficients
- MayerDFDTSpherical(Potential2Spherical) - Constructor for class etomica.virial.MayerDFDTSpherical
-
Constructor for MayerESpherical.
- MayerDFQFHDTSpherical - Class in etomica.virial
-
Required for computing temperature derivatives of virial coefficients computed with quadratic Feynmann-Hibbs modification
to the potential.
- MayerDFQFHDTSpherical(P2EffectiveFeynmanHibbs) - Constructor for class etomica.virial.MayerDFQFHDTSpherical
-
Constructor for MayerESpherical.
- MayerEGeneral - Class in etomica.virial
-
- MayerEGeneral(IPotentialMolecular) - Constructor for class etomica.virial.MayerEGeneral
-
Constructor Mayer function using given potential.
- MayerEHardSphere - Class in etomica.virial
-
- MayerEHardSphere() - Constructor for class etomica.virial.MayerEHardSphere
-
Constructor for MayerEHardSphere.
- MayerEHardSphere(double) - Constructor for class etomica.virial.MayerEHardSphere
-
- MayerENonGeneral - Class in etomica.virial
-
- MayerENonGeneral(IPotentialMolecular, double) - Constructor for class etomica.virial.MayerENonGeneral
-
Constructor Mayer function using given potential.
- MayerESpherical - Class in etomica.virial
-
- MayerESpherical(Potential2Spherical) - Constructor for class etomica.virial.MayerESpherical
-
Constructor for MayerESpherical.
- MayerFunction - Interface in etomica.virial
-
- MayerFunctionMolecularThreeBody - Class in etomica.virial
-
- MayerFunctionMolecularThreeBody(IPotentialMolecular) - Constructor for class etomica.virial.MayerFunctionMolecularThreeBody
-
- MayerFunctionNonAdditive - Interface in etomica.virial
-
Interface for a Mayer f-function, which takes 3+ atoms and
returns exp(-(u(atoms)-u(pairs))/kT) - 1
- MayerFunctionNonAdditiveFull - Class in etomica.virial
-
- MayerFunctionNonAdditiveFull(IPotentialMolecular) - Constructor for class etomica.virial.MayerFunctionNonAdditiveFull
-
- MayerFunctionProductGeneral - Class in etomica.virial
-
- MayerFunctionProductGeneral(Space, MayerFunction[], double[]) - Constructor for class etomica.virial.MayerFunctionProductGeneral
-
- MayerFunctionSphericalThreeBody - Class in etomica.virial
-
Non-additive Mayer function class for "spherical" potentials
- MayerFunctionSphericalThreeBody(IPotentialAtomicMultibody) - Constructor for class etomica.virial.MayerFunctionSphericalThreeBody
-
- MayerFunctionSum - Class in etomica.virial
-
- MayerFunctionSum(MayerFunction[], double[]) - Constructor for class etomica.virial.MayerFunctionSum
-
- MayerFunctionSumGeneral - Class in etomica.virial
-
- MayerFunctionSumGeneral(Space, MayerFunction[], double[]) - Constructor for class etomica.virial.MayerFunctionSumGeneral
-
- MayerFunctionTemperature - Class in etomica.virial
-
Mayer function that wraps another MayerFunction and ignores
the temperature passed to f(), asking the wrapped MayerFunction
for its value at the MayerFunction Temperature's temperature.
- MayerFunctionTemperature(MayerFunction, double) - Constructor for class etomica.virial.MayerFunctionTemperature
-
- MayerFunctionThreeBody - Class in etomica.virial
-
This class acts as a non-additive Mayer function for molecules that
interact with only a 3-body potential.
- MayerFunctionThreeBody() - Constructor for class etomica.virial.MayerFunctionThreeBody
-
- MayerGeneral - Class in etomica.virial
-
- MayerGeneral(IPotentialMolecular) - Constructor for class etomica.virial.MayerGeneral
-
Constructor Mayer function using given potential.
- MayerGeneralAtomic - Class in etomica.virial
-
- MayerGeneralAtomic(IPotentialAtomic) - Constructor for class etomica.virial.MayerGeneralAtomic
-
Constructor Mayer function using given potential.
- MayerGeneralSpherical - Class in etomica.virial
-
- MayerGeneralSpherical(Potential2Spherical) - Constructor for class etomica.virial.MayerGeneralSpherical
-
Constructor Mayer function using given potential.
- MayerHardSphere - Class in etomica.virial
-
- MayerHardSphere() - Constructor for class etomica.virial.MayerHardSphere
-
Constructor for MayerHardSphere.
- MayerHardSphere(double) - Constructor for class etomica.virial.MayerHardSphere
-
- MayerHSMixture - Class in etomica.virial
-
This class represents a Mayer function for any pair of species from a
hard sphere mixture.
- MayerHSMixture(int, double[][], double, boolean, Space) - Constructor for class etomica.virial.MayerHSMixture
-
- MayerIonicDiagram1qbond - Class in etomica.virial.cluster
-
modified from WertheimNaphthalene class
cluster diagrams generator for ionic solutions, based on Mayer's theory
f-bond is splitted to k-bond, (kg1+g1)
diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded)
g1/kg1 is magically changed to represent q1-bond [exp(-kappa * r / (4*pi*r)] with different domain, but g1 is still in use
kg1 represents [exp(-kappa * r / (4*pi*r)] instead of [exp(-alpha * r / (4*pi*r)] (kq1 essentially)
===> then q1 is substituted by (xq1-kg1), where xq1 has domain:[sigmaHS, infinity]
qi represent xqi bonds, gi represent REAL q bonds
the final result contains q1(represent xq1) and kg1(represent q1)
can handle 4pt
just xq1 & kq1 & k in the final set of S
- MayerIonicDiagram1qbond(int, boolean, boolean, int, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- MayerIonicDiagram1qbond(int, boolean, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- MayerIonicDiagram2qbonds - Class in etomica.virial.cluster
-
Mayer's theory on ionic solution
f-bond is splitted to k-bond, (kg+g),(kg2+g2)
diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded)
gi is substituted by (qi - kgi)
qi represent modified q bonds, gi represent REAL q bonds
even number of q bonds , the final result contains q1,q2,kg1,kg2bonds
- MayerIonicDiagram2qbonds(int, boolean, boolean, int, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- MayerIonicDiagram2qbonds(int, boolean, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- MayerIonicDiagram4qbonds - Class in etomica.virial.cluster
-
cluster diagrams generator for ionic solutions, based on Mayer's theory
f-bond is split into k-bond(HS f-hond), (kg+g),(kg2+g2),(kg3+g3),(kg4+g4)truncation
diagrams with g chain(s) are reduced to lower order of diagrams(here they are just simply discarded)
gi is substituted by (qi - kgi), where qi represents modified q bonds( domain [sigmaHS,infinity), gi represent REAL q bonds, i represents q bonds power
the final sets of diagrams contains q1,q2,q3,q4;kg1,kg2,kg3,kg4 bonds
2 pt diagrams with q2 bond is discarded ( cycle diagram)
cannot handle 4 points due to the insufficiency of calculations
- MayerIonicDiagram4qbonds(int, boolean, boolean, int, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- MayerIonicDiagram4qbonds(int, boolean, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- MayerPTAtt - Class in etomica.virial
-
Mayer function class that returns temperature expansion bond of the desired
order using molecular potentials.
- MayerPTAtt(IPotentialMolecular, IPotentialMolecular, int) - Constructor for class etomica.virial.MayerPTAtt
-
Constructor takes reference potential, attractive component and order in temperature.
- MayerPUGeneral - Class in etomica.virial
-
f + u
f: exp(-beta U)
u: 0 for r < sigmaHS, dipole energy otherwise
a Potential2 object.
- MayerPUGeneral(Space, double, double, IPotentialMolecular) - Constructor for class etomica.virial.MayerPUGeneral
-
- MayerSphericalPlus - Class in etomica.virial
-
- MayerSphericalPlus(Potential2Spherical, Potential2Spherical) - Constructor for class etomica.virial.MayerSphericalPlus
-
Constructor Mayer function using given potential.
- MayerSphericalPTAtt - Class in etomica.virial
-
Mayer function class that returns temperature expansion bond of the desired
order.
- MayerSphericalPTAtt(Potential2Spherical, Potential2Spherical, int) - Constructor for class etomica.virial.MayerSphericalPTAtt
-
Constructor takes reference potential, attractive component and order in temperature.
- MayerSSSeries - Class in etomica.virial
-
- MayerSSSeries(int) - Constructor for class etomica.virial.MayerSSSeries
-
Constructor for MayerHardSphere.
- MayerWell - Class in etomica.virial
-
- MayerWell(double, double) - Constructor for class etomica.virial.MayerWell
-
- MayerXSpherical - Class in etomica.virial
-
- MayerXSpherical(Potential2SoftSpherical) - Constructor for class etomica.virial.MayerXSpherical
-
Constructor for MayerESpherical.
- mBond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- mBond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- mBond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- mBond - Variable in class etomica.virial.cluster.VirialDiagrams.ArticulatedAt0
-
- mBond - Variable in class etomica.virial.cluster.VirialDiagrams
-
- mBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- MBond - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- mBond - Variable in class etomica.virial.cluster.VirialDiagramsPT.ArticulatedAt0
-
- mBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- mBond - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- mBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- mc - Variable in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
- mc - Variable in class etomica.virial.ClusterWheatleySoftBD
-
- mc - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- mc - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- mc - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- mCapF1Bond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- mCapF2Bond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- mCapFACBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- mCapFACBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- mCapFBCBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- mCapFBCBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- mCapFBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- mCapFCABond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- mCapFCABond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- mCapFCBBond - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- mCapFCBBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- mCluster - Variable in class etomica.virial.cluster.ClusterGenerator
-
- MCMove - Class in etomica.integrator.mcmove
-
Parent class for all elementary Monte Carlo move classes, as used by
IntegratorMC class.
- MCMove(PotentialMaster) - Constructor for class etomica.integrator.mcmove.MCMove
-
- MCMove(PotentialMaster, MCMoveTracker) - Constructor for class etomica.integrator.mcmove.MCMove
-
- mcMove - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- mcMove - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
-
- mcMove - Variable in class etomica.interfacial.LJMD
-
- mcMove - Variable in class etomica.normalmode.MeterSamplingHarmonic
-
- mcMove - Variable in class etomica.normalmode.MeterSamplingTarget
-
- mcMove - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- mcMove - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- mcmove - Variable in class etomica.spin.Heisenberg
-
- mcMove - Variable in class etomica.virial.MCMoveClusterAtomQ
-
- mcMoveAtom - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- mcMoveAtom - Variable in class etomica.densityofstate.DensityOfState
-
- mcMoveAtom - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
-
- mcMoveAtom - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- mcMoveAtom - Variable in class etomica.freeenergy.npath.SimLJ
-
- MCMoveAtom - Class in etomica.integrator.mcmove
-
Standard Monte Carlo atom-displacement trial move.
- MCMoveAtom(IRandom, PotentialMaster, Space) - Constructor for class etomica.integrator.mcmove.MCMoveAtom
-
Constructs the move with default stepSize = 1.0, stepSizeMax = 15.0, fixOverlap = false
- MCMoveAtom(IRandom, PotentialMaster, Space, double, double, boolean) - Constructor for class etomica.integrator.mcmove.MCMoveAtom
-
- MCMoveAtom(IRandom, PotentialMaster, Space, double, double, boolean, MeterPotentialEnergy) - Constructor for class etomica.integrator.mcmove.MCMoveAtom
-
- mcMoveAtom - Variable in class etomica.liquidLJ.LjMC3D
-
- mcMoveAtom - Variable in class etomica.metastable.LJNPT
-
- mcMoveAtom - Variable in class etomica.metastable.LJNVT
-
- mcMoveAtom - Variable in class etomica.modules.ensembles.LJMC
-
- mcMoveAtom - Variable in class etomica.simulation.prototypes.HSMC2D
-
- mcMoveAtom - Variable in class etomica.simulation.prototypes.SoftSphere3d
-
- mcMoveAtom - Variable in class etomica.surfacetension.LJMC
-
- mcMoveAtom - Variable in class etomica.tests.TestLJGCMC3D
-
- mcMoveAtom - Variable in class etomica.tests.TestLJMC3D
-
- mcMoveAtom - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- mcMoveAtom - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- mcMoveAtom - Variable in class etomica.yukawa.TestHC2YukawaMC3D
-
- mcMoveAtom - Variable in class etomica.yukawa.TestYukawaMC3D
-
- MCMoveAtomAdjacent - Class in etomica.modules.entropylottery
-
Monte Carlo move that moves an atom by +/- 1 unit in a random dimension.
- MCMoveAtomAdjacent(IRandom, Space) - Constructor for class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- mcMoveAtomBigStep - Variable in class etomica.surfacetension.LJMC
-
- MCMoveAtomCoupled - Class in etomica.freeenergy.npath
-
Created by andrew on 4/11/17.
- MCMoveAtomCoupled(IRandom, PotentialMaster, Space) - Constructor for class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- MCMoveAtomCoupled(PotentialMaster, IRandom, Space, double, double, boolean) - Constructor for class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- MCMoveAtomCoupled(PotentialMaster, MeterPotentialEnergy, IRandom, Space, double, double, boolean) - Constructor for class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- mcMoveAtomCoupled - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- mcMoveAtomCoupled - Variable in class etomica.freeenergy.npath.SimLJ
-
- MCMoveAtomCoupled - Class in etomica.normalmode
-
Standard Monte Carlo atom-displacement trial move.
- MCMoveAtomCoupled(PotentialMaster, MeterPotentialEnergy, IRandom, Space) - Constructor for class etomica.normalmode.MCMoveAtomCoupled
-
- MCMoveAtomCoupledBennet - Class in etomica.normalmode
-
Standard Monte Carlo atom-displacement trial move.
- MCMoveAtomCoupledBennet(PotentialMaster, IRandom, CoordinateDefinition, NormalModes, double, Space) - Constructor for class etomica.normalmode.MCMoveAtomCoupledBennet
-
- MCMoveAtomCoupledUmbrella - Class in etomica.normalmode
-
Standard Monte Carlo atom-displacement trial move.
- MCMoveAtomCoupledUmbrella(PotentialMaster, IRandom, CoordinateDefinition, NormalModes, double, Space) - Constructor for class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- MCMoveAtomDimer - Class in etomica.association
-
- MCMoveAtomDimer(Simulation, PotentialMaster, Space) - Constructor for class etomica.association.MCMoveAtomDimer
-
- MCMoveAtomDimer(PotentialMaster, IRandom, Space, double, double, boolean) - Constructor for class etomica.association.MCMoveAtomDimer
-
- mcMoveAtomDimer - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- mcMoveAtomDimer - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- MCMoveAtomInRegion - Class in etomica.integrator.mcmove
-
MC move that operates only on atoms within a given region of x values.
- MCMoveAtomInRegion(IRandom, PotentialMaster, Space) - Constructor for class etomica.integrator.mcmove.MCMoveAtomInRegion
-
- MCMoveAtomMonomer - Class in etomica.association
-
- MCMoveAtomMonomer(Simulation, PotentialMaster, Space) - Constructor for class etomica.association.MCMoveAtomMonomer
-
- MCMoveAtomMonomer(PotentialMaster, IRandom, Space, double, double, boolean) - Constructor for class etomica.association.MCMoveAtomMonomer
-
- mcMoveAtomMonomer - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- mcMoveAtomMonomer - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- mcMoveAtomMonomer - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- mcMoveAtomMonomer - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- MCMoveAtomNbr - Class in etomica.interfacial
-
- MCMoveAtomNbr(IRandom, PotentialMaster, Space) - Constructor for class etomica.interfacial.MCMoveAtomNbr
-
- MCMoveAtomNoSmer - Class in etomica.association
-
- MCMoveAtomNoSmer(IRandom, PotentialMaster, Space) - Constructor for class etomica.association.MCMoveAtomNoSmer
-
- MCMoveAtomNPath - Class in etomica.freeenergy.npath
-
Created by andrew on 4/11/17.
- MCMoveAtomNPath(IRandom, PotentialMaster, Space, P1ImageHarmonic) - Constructor for class etomica.freeenergy.npath.MCMoveAtomNPath
-
- MCMoveAtomSmer - Class in etomica.association
-
- MCMoveAtomSmer(Simulation, PotentialMaster, Space) - Constructor for class etomica.association.MCMoveAtomSmer
-
- MCMoveAtomSmer(PotentialMaster, IRandom, Space, double, double, boolean) - Constructor for class etomica.association.MCMoveAtomSmer
-
- mcMoveAtomSmer - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- mcMoveAtomSmer - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- MCMoveAtomSuperBox - Class in etomica.normalmode
-
Standard Monte Carlo atom-displacement trial move.
- MCMoveAtomSuperBox(PotentialMaster, IRandom, Space, CoordinateDefinitionLeafSuperBox) - Constructor for class etomica.normalmode.MCMoveAtomSuperBox
-
- MCMoveAtomSwap - Class in etomica.freeenergy.npath
-
Created by andrew on 4/11/17.
- MCMoveAtomSwap(IRandom, PotentialMaster, Space, P1ImageHarmonic) - Constructor for class etomica.freeenergy.npath.MCMoveAtomSwap
-
- mcMoveBiasUB - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- MCMoveBiasUB - Class in etomica.association
-
- MCMoveBiasUB(PotentialMasterCell, BiasVolume, IRandom, Space) - Constructor for class etomica.association.MCMoveBiasUB
-
- mcMoveBiasUB - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- mcMoveBiasUB - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- mcMoveBiasUB - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- mcMoveBiasUB - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- MCMoveBiasUBMolecule - Class in etomica.association
-
- MCMoveBiasUBMolecule(PotentialMaster, BiasVolumeMolecule, IRandom, Space) - Constructor for class etomica.association.MCMoveBiasUBMolecule
-
- MCMoveBox - Class in etomica.integrator.mcmove
-
MCMove parent class for moves that operate on a single Box.
- MCMoveBox(PotentialMaster) - Constructor for class etomica.integrator.mcmove.MCMoveBox
-
- MCMoveBox(PotentialMaster, MCMoveTracker) - Constructor for class etomica.integrator.mcmove.MCMoveBox
-
- MCMoveBoxSize - Class in etomica.integrator.mcmove
-
Monte Carlo move for changing the box dimensions at constant volume.
- MCMoveBoxSize(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.mcmove.MCMoveBoxSize
-
- MCMoveBoxSize(PotentialMaster, IRandom, Space) - Constructor for class etomica.integrator.mcmove.MCMoveBoxSize
-
- MCMoveBoxStep - Class in etomica.integrator.mcmove
-
MCMove parent class for moves that have a step size and operate on a single
Box.
- MCMoveBoxStep(PotentialMaster) - Constructor for class etomica.integrator.mcmove.MCMoveBoxStep
-
- MCMoveBoxStep(PotentialMaster, MCMoveStepTracker) - Constructor for class etomica.integrator.mcmove.MCMoveBoxStep
-
- MCMoveCBMC - Class in etomica.models.hexane
-
- MCMoveCBMC(PotentialMaster, IRandom, Space, IntegratorMC, Box, int, int) - Constructor for class etomica.models.hexane.MCMoveCBMC
-
- MCMoveChangeBondLength - Class in etomica.virial
-
- MCMoveChangeBondLength(PotentialMaster, IRandom, Space, double) - Constructor for class etomica.virial.MCMoveChangeBondLength
-
- MCMoveChangeMultipleModes - Class in etomica.models.oneDHardRods
-
A Monte Carlo move which selects a wave vector and mode(s), and changes the normal mode
associated with that wave vector and mode(s).
- MCMoveChangeMultipleModes(PotentialMaster, IRandom) - Constructor for class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- MCMoveChangeMultipleWV - Class in etomica.models.oneDHardRods
-
A Monte Carlo move which selects a wave vector, and changes the normal modes
associated with that wave vector.
- MCMoveChangeMultipleWV(PotentialMaster, IRandom) - Constructor for class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- MCMoveClusterAngleBend - Class in etomica.virial
-
An MC Move for cluster simulations that bends the bond angle for 3-atom
molecule.
- MCMoveClusterAngleBend(Simulation, PotentialMaster, Space) - Constructor for class etomica.virial.MCMoveClusterAngleBend
-
- MCMoveClusterAngleBend(PotentialMaster, IRandom, double, Space) - Constructor for class etomica.virial.MCMoveClusterAngleBend
-
- MCMoveClusterAngleBendAceticAcid - Class in etomica.virial
-
An MC Move for cluster simulations that bends the bond angle for 3-atom
molecule.
- MCMoveClusterAngleBendAceticAcid(Simulation, PotentialMaster, Space) - Constructor for class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- MCMoveClusterAngleBendAceticAcid(PotentialMaster, IRandom, double, Space) - Constructor for class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- MCMoveClusterAtom - Class in etomica.virial
-
Overrides MCMoveAtom to prevent index-0 molecule from being displaced
- MCMoveClusterAtom(IRandom, Space) - Constructor for class etomica.virial.MCMoveClusterAtom
-
- MCMoveClusterAtomChainHSTail - Class in etomica.virial
-
Grows configurations of chains with the pair probability distribution that
is flat for some distance and then has a power-law decay tail.
- MCMoveClusterAtomChainHSTail(IRandom, Space, double, double) - Constructor for class etomica.virial.MCMoveClusterAtomChainHSTail
-
- MCMoveClusterAtomDiscrete - Class in etomica.virial
-
Extension of MCMoveClusterAtom that moves only the second atom and only
along the x axis.
- MCMoveClusterAtomDiscrete(IRandom, Space, double) - Constructor for class etomica.virial.MCMoveClusterAtomDiscrete
-
- MCMoveClusterAtomHSChain - Class in etomica.virial
-
Class that samples molecule positions based on a chain of hard spheres of
diameter sigma.
- MCMoveClusterAtomHSChain(IRandom, Space, double) - Constructor for class etomica.virial.MCMoveClusterAtomHSChain
-
- MCMoveClusterAtomHSChainMix - Class in etomica.virial
-
Class that samples molecule positions based on a chain of hard spheres of
various sizes.
- MCMoveClusterAtomHSChainMix(IRandom, Space, double[][]) - Constructor for class etomica.virial.MCMoveClusterAtomHSChainMix
-
- MCMoveClusterAtomHSRing - Class in etomica.virial
-
- MCMoveClusterAtomHSRing(IRandom, Space, double) - Constructor for class etomica.virial.MCMoveClusterAtomHSRing
-
- MCMoveClusterAtomHSTree - Class in etomica.virial
-
Class that samples molecule positions based on a tree of hard spheres of
diameter sigma.
- MCMoveClusterAtomHSTree(IRandom, Space, double) - Constructor for class etomica.virial.MCMoveClusterAtomHSTree
-
- MCMoveClusterAtomHSTreeMix - Class in etomica.virial
-
Class that samples molecule positions based on a tree of hard spheres of
various sizes.
- MCMoveClusterAtomHSTreeMix(IRandom, Space, double[][]) - Constructor for class etomica.virial.MCMoveClusterAtomHSTreeMix
-
- MCMoveClusterAtomMulti - Class in etomica.virial
-
- MCMoveClusterAtomMulti(IRandom, Space) - Constructor for class etomica.virial.MCMoveClusterAtomMulti
-
- MCMoveClusterAtomQ - Class in etomica.virial
-
- MCMoveClusterAtomQ(IRandom, Space, MCMoveAtom) - Constructor for class etomica.virial.MCMoveClusterAtomQ
-
- MCMoveClusterAtomRotateMulti - Class in etomica.virial
-
Extension of MCMoveAtom that does trial in which several atom orientations are
perturbed.
- MCMoveClusterAtomRotateMulti(IRandom, Space) - Constructor for class etomica.virial.MCMoveClusterAtomRotateMulti
-
- MCMoveClusterAtomSQWChain - Class in etomica.virial
-
- MCMoveClusterAtomSQWChain(IRandom, Space, double, double) - Constructor for class etomica.virial.MCMoveClusterAtomSQWChain
-
- MCMoveClusterAtomSQWTree - Class in etomica.virial
-
- MCMoveClusterAtomSQWTree(IRandom, Space, double, double) - Constructor for class etomica.virial.MCMoveClusterAtomSQWTree
-
- MCMoveClusterDiagram - Class in etomica.virial
-
Move that attempts to perform changes in the cluster diagram.
- MCMoveClusterDiagram(PotentialMaster) - Constructor for class etomica.virial.MCMoveClusterDiagram
-
- MCMoveClusterMolecule - Class in etomica.virial
-
Standard Monte Carlo molecule-displacement trial move for cluster integrals.
- MCMoveClusterMolecule(Simulation, Space) - Constructor for class etomica.virial.MCMoveClusterMolecule
-
- MCMoveClusterMolecule(IRandom, Space, double) - Constructor for class etomica.virial.MCMoveClusterMolecule
-
- MCMoveClusterMoleculeLayerMove - Class in etomica.virial
-
Monte Carlo molecule-displacement from 1 layer to the other layer trial move for cluster integrals.
- MCMoveClusterMoleculeLayerMove(Simulation, Space) - Constructor for class etomica.virial.MCMoveClusterMoleculeLayerMove
-
- MCMoveClusterMoleculeMulti - Class in etomica.virial
-
- MCMoveClusterMoleculeMulti(Simulation, Space) - Constructor for class etomica.virial.MCMoveClusterMoleculeMulti
-
- MCMoveClusterMoleculeMulti(PotentialMaster, IRandom, Space, double) - Constructor for class etomica.virial.MCMoveClusterMoleculeMulti
-
- MCMoveClusterPolyhedraChain - Class in etomica.virial
-
- MCMoveClusterPolyhedraChain(IRandom, Space, double, IPotentialAtomic, double[][]) - Constructor for class etomica.virial.MCMoveClusterPolyhedraChain
-
- MCMoveClusterPolyhedraTree - Class in etomica.virial
-
- MCMoveClusterPolyhedraTree(IRandom, Space, double, IPotentialAtomic, double[][]) - Constructor for class etomica.virial.MCMoveClusterPolyhedraTree
-
- MCMoveClusterReptateMulti - Class in etomica.virial
-
An MC move for cluster simulations which performs reptation moves on molecules.
- MCMoveClusterReptateMulti(Simulation, PotentialMaster, int) - Constructor for class etomica.virial.MCMoveClusterReptateMulti
-
- MCMoveClusterReptateMulti(PotentialMaster, IRandom, int) - Constructor for class etomica.virial.MCMoveClusterReptateMulti
-
- MCMoveClusterRingPartialRegrow - Class in etomica.virial
-
MCMove that partially regrows the beads of a ring polymer, accepting or
rejecting the move based on the sampling weight.
- MCMoveClusterRingPartialRegrow(PotentialMaster, IRandom, Space) - Constructor for class etomica.virial.MCMoveClusterRingPartialRegrow
-
- MCMoveClusterRingPartialRegrow(PotentialMaster, IRandom, Space, int[][]) - Constructor for class etomica.virial.MCMoveClusterRingPartialRegrow
-
- MCMoveClusterRingRegrow - Class in etomica.virial
-
MCMove that fully regrows the beads of a ring polymer, accepting or
rejecting the move based on the sampling weight.
- MCMoveClusterRingRegrow(IRandom, Space) - Constructor for class etomica.virial.MCMoveClusterRingRegrow
-
- MCMoveClusterRingRegrow(IRandom, Space, int[][]) - Constructor for class etomica.virial.MCMoveClusterRingRegrow
-
- MCMoveClusterRingRegrowExchange - Class in etomica.virial
-
MCMove that fully regrows the beads of a ring polymer, accepting or
rejecting the move based on the sampling weight.
- MCMoveClusterRingRegrowExchange(IRandom, Space) - Constructor for class etomica.virial.MCMoveClusterRingRegrowExchange
-
- MCMoveClusterRingRegrowOrientation - Class in etomica.virial
-
MCMove that fully regrows the beads of a ring polymer by rotating the images, accepting or
rejecting the move based on the sampling weight.
- MCMoveClusterRingRegrowOrientation(IRandom, Space, int) - Constructor for class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- MCMoveClusterRingScale - Class in etomica.virial
-
MCMove that scales the atoms of a molecule in or out.
- MCMoveClusterRingScale(PotentialMaster, IRandom, Space) - Constructor for class etomica.virial.MCMoveClusterRingScale
-
- MCMoveClusterRingScale(PotentialMaster, IRandom, Space, int[][]) - Constructor for class etomica.virial.MCMoveClusterRingScale
-
- MCMoveClusterRotateCH3 - Class in etomica.virial
-
Monte Carlo CH3 rotation for cluster integrals(Alkane TraPPE-EH).
- MCMoveClusterRotateCH3(Simulation, PotentialMaster, int, Space) - Constructor for class etomica.virial.MCMoveClusterRotateCH3
-
- MCMoveClusterRotateCH3(PotentialMaster, IRandom, double, int, Space) - Constructor for class etomica.virial.MCMoveClusterRotateCH3
-
- MCMoveClusterRotateMolecule3D - Class in etomica.virial
-
MC move for Mayer Sampling that rotates a single molecule
- MCMoveClusterRotateMolecule3D(PotentialMaster, IRandom, Space) - Constructor for class etomica.virial.MCMoveClusterRotateMolecule3D
-
- MCMoveClusterRotateMoleculeMulti - Class in etomica.virial
-
MCMove for use in a Mayer sampling simulation that rotates all molecules in
a Box except the first molecule, which is never moved.
- MCMoveClusterRotateMoleculeMulti(IRandom, Space) - Constructor for class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- MCMoveClusterTorsionAceticAcid - Class in etomica.virial
-
An MC Move for cluster simulations that performs torsion moves on acetic acid.
- MCMoveClusterTorsionAceticAcid(PotentialMaster, Space, IRandom) - Constructor for class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- MCMoveClusterTorsionAlkaneEH - Class in etomica.virial
-
MC move for alkane-TraPPE-EH torsion
pick up carbons in the box only, but move update all the atoms(carbons and hydrogens)
- MCMoveClusterTorsionAlkaneEH(Simulation, PotentialMaster, Space, P4BondTorsion) - Constructor for class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- MCMoveClusterTorsionAlkaneEH(PotentialMaster, Space, IRandom, double, P4BondTorsion, int) - Constructor for class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- MCMoveClusterTorsionMulti - Class in etomica.virial
-
An MC Move for cluster simulations that performs torsion moves on a chain
molecule (of length N>=4).
- MCMoveClusterTorsionMulti(Simulation, PotentialMaster, Space, P4BondTorsion) - Constructor for class etomica.virial.MCMoveClusterTorsionMulti
-
- MCMoveClusterTorsionMulti(PotentialMaster, Space, IRandom, double, P4BondTorsion, int) - Constructor for class etomica.virial.MCMoveClusterTorsionMulti
-
- MCMoveClusterWiggleAceticAcid - Class in etomica.virial
-
An MC Move for cluster simulations that "wiggles" a chain molecule.
- MCMoveClusterWiggleAceticAcid(Simulation, PotentialMaster, Space) - Constructor for class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- MCMoveClusterWiggleAceticAcid(PotentialMaster, IRandom, double, Space) - Constructor for class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- MCMoveClusterWiggleAlkaneEH - Class in etomica.virial
-
Wiggle move for alkane, TraPPE-EH
hydrogens attached to the 3 carbons are updated, keeping bond lengths and angles fixed
*********** outline ************
// update j if j == 0 or j == n-1
// update 3 H on j
// if j==0, update 2H on (j+1)
// if j==n-1, update 2H on (j-1)
&& 0
- MCMoveClusterWiggleAlkaneEH(Simulation, PotentialMaster, int, Space) - Constructor for class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- MCMoveClusterWiggleAlkaneEH(PotentialMaster, IRandom, double, int, Space) - Constructor for class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
Constructor for MCMoveAtomMulti.
- MCMoveClusterWiggleMulti - Class in etomica.virial
-
An MC Move for cluster simulations that "wiggles" a chain molecule.
- MCMoveClusterWiggleMulti(Simulation, PotentialMaster, int, Space) - Constructor for class etomica.virial.MCMoveClusterWiggleMulti
-
- MCMoveClusterWiggleMulti(PotentialMaster, IRandom, double, int, Space) - Constructor for class etomica.virial.MCMoveClusterWiggleMulti
-
- MCMoveCombinedCbmcTranslation - Class in etomica.models.hexane
-
MC move which performs a configuration bias monte carlo moved, then moves
that atom to a new position so that its center of mass does not change.
- MCMoveCombinedCbmcTranslation(PotentialMaster, MCMoveCBMC, IRandom, Space) - Constructor for class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- MCMoveCombinedCbmcTranslation(PotentialMaster, MCMoveCBMC, IRandom, Box, Space) - Constructor for class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- MCMoveCompareMultipleWV - Class in etomica.models.oneDHardRods
-
A Monte Carlo move which compares several normal modes to harmonic normal
modes and then explores the phase space defined by the remaining normal
modes.
- MCMoveCompareMultipleWV(PotentialMaster, IRandom) - Constructor for class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- mcMoveDiagram - Variable in class etomica.virial.simulations.SimulationVirialDiagram
-
- MCMoveDimer - Class in etomica.association
-
Standard Monte Carlo atom-displacement trial move of dimer
- MCMoveDimer(Simulation, PotentialMasterCell, Space, IPotentialAtomic) - Constructor for class etomica.association.MCMoveDimer
-
- MCMoveDimer(PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.association.MCMoveDimer
-
- mcMoveDimer - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- mcMoveDimer - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- MCMoveDimer - Class in etomica.integrator.mcmove
-
Standard Monte Carlo atom-displacement trial move.
- MCMoveDimer(Simulation, PotentialMasterCell, Space, IPotentialAtomic) - Constructor for class etomica.integrator.mcmove.MCMoveDimer
-
- MCMoveDimer(PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.integrator.mcmove.MCMoveDimer
-
- mcMoveDimer - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- MCMoveDimerRotate - Class in etomica.association
-
Standard Monte Carlo atom-displacement trial move.
- MCMoveDimerRotate(Simulation, PotentialMasterCell, Space, IPotentialAtomic) - Constructor for class etomica.association.MCMoveDimerRotate
-
- MCMoveDimerRotate(PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.association.MCMoveDimerRotate
-
- mcMoveDimerRotate - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- mcMoveDimerRotate - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- MCMoveDimerRotate - Class in etomica.integrator.mcmove
-
Standard Monte Carlo atom-displacement trial move.
- MCMoveDimerRotate(Simulation, PotentialMasterCell, Space, IPotentialAtomic) - Constructor for class etomica.integrator.mcmove.MCMoveDimerRotate
-
- MCMoveDimerRotate(PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.integrator.mcmove.MCMoveDimerRotate
-
- mcMoveDimerRotate - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- MCMoveEinsteinCrystal - Class in etomica.normalmode
-
MC move whose purpose in life is to sample an Einstein crystal.
- MCMoveEinsteinCrystal(Space, IRandom) - Constructor for class etomica.normalmode.MCMoveEinsteinCrystal
-
- MCMoveEvent - Class in etomica.integrator.mcmove
-
- MCMoveEvent() - Constructor for class etomica.integrator.mcmove.MCMoveEvent
-
- MCMoveHarmonic - Class in etomica.normalmode
-
- MCMoveHarmonic(IRandom) - Constructor for class etomica.normalmode.MCMoveHarmonic
-
- mcMoveHarmonic - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
-
- mcMoveHarmonic - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- mcMoveHarmonic - Variable in class etomica.normalmode.MeterHarmonicEnergyFromMove
-
- mcMoveHarmonic - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
-
- mcMoveHarmonic - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- mcMoveHarmonic - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- MCMoveHarmonicEin - Class in etomica.normalmode
-
MC move whose purpose in life is to sample a system whose energy is a
combination of normal mode contributions and Einstein crystal
contributions.
- MCMoveHarmonicEin(IRandom) - Constructor for class etomica.normalmode.MCMoveHarmonicEin
-
- MCMoveHarmonicStep - Class in etomica.normalmode
-
MCMove that performs random displacements in the harmonic coordinates for
the k=0 wave vector.
- MCMoveHarmonicStep(PotentialMaster, IRandom) - Constructor for class etomica.normalmode.MCMoveHarmonicStep
-
- mcMoveHarmonicStep - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- mcMoveHarmonicStep - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- mcMoveID - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- mcMoveID - Variable in class etomica.metastable.LJmuVT
-
- mcMoveID - Variable in class etomica.modules.ensembles.LJMC
-
- mcMoveID - Variable in class etomica.normalmode.DataSourceImposedFEFit
-
- mcMoveID - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
-
- mcMoveID - Variable in class etomica.normalmode.SimHSMDVacancy
-
- mcMoveID - Variable in class etomica.normalmode.SimLJVacancy
-
- mcMoveID - Variable in class etomica.tests.TestLJGCMC3D
-
- mcMoveIDA - Variable in class etomica.modules.adsorption.Adsorption
-
- mcMoveIDB - Variable in class etomica.modules.adsorption.Adsorption
-
- MCMoveIDBiasAction - Class in etomica.integrator.mcmove
-
IAction which takes data from an MCMoveOverlapListener about acceptance
probabilities for insert/delete moves and uses them to update biasing of
the move.
- MCMoveIDBiasAction(IntegratorMC, MCMoveInsertDeleteBiased, int, double, MCMoveOverlapListener, int) - Constructor for class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- MCMoveInsertDelete - Class in etomica.integrator.mcmove
-
Elementary Monte Carlo move in which a molecule of a specified species is
inserted into or removed from a box.
- MCMoveInsertDelete(PotentialMaster, IRandom, Space) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDelete
-
- MCMoveInsertDeleteBiased - Class in etomica.integrator.mcmove
-
Biased MCMove for insertion and deletion.
- MCMoveInsertDeleteBiased(PotentialMaster, IRandom, Space, int, int) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- MCMoveInsertDeleteLatticeVacancy - Class in etomica.integrator.mcmove
-
Looks for atoms without a full set of first nearest neighbors and attempts
insertions adjacent to one of those atoms.
- MCMoveInsertDeleteLatticeVacancy(PotentialMaster, IRandom, Space, Integrator, double, int, int) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce - Class in etomica.integrator.mcmove
-
- MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr - Class in etomica.integrator.mcmove
-
- MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell - Class in etomica.integrator.mcmove
-
- MCMoveInsertDeleteVacancy - Class in etomica.integrator.mcmove
-
Looks for atoms without a full set of first nearest neighbors and attempts
insertions adjacent to one of those atoms.
- MCMoveInsertDeleteVacancy(PotentialMaster, IRandom, Space, Integrator, double, int, int) - Constructor for class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- mcMoveList - Variable in class etomica.integrator.mcmove.MCMoveManager
-
- MCMoveManager - Class in etomica.integrator.mcmove
-
- MCMoveManager(IRandom) - Constructor for class etomica.integrator.mcmove.MCMoveManager
-
- MCMoveMolecular - Interface in etomica.integrator.mcmove
-
An interface that contains MoleculeIterator
- MCMoveMolecule - Class in etomica.integrator.mcmove
-
Standard Monte Carlo molecule-displacement trial move.
- MCMoveMolecule(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.mcmove.MCMoveMolecule
-
- MCMoveMolecule(PotentialMaster, IRandom, Space, double, double) - Constructor for class etomica.integrator.mcmove.MCMoveMolecule
-
- mcMoveMolecule - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- mcMoveMolecule - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- mcMoveMolecule - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- MCMoveMoleculeCoupled - Class in etomica.normalmode
-
Standard Monte Carlo molecule-displacement trial move.
- MCMoveMoleculeCoupled(PotentialMaster, IRandom, Space) - Constructor for class etomica.normalmode.MCMoveMoleculeCoupled
-
- MCMoveMoleculeCoupledDLPOLY - Class in etomica.paracetamol
-
Standard Monte Carlo molecule-displacement trial move.
- MCMoveMoleculeCoupledDLPOLY(PotentialMaster, IRandom, Space) - Constructor for class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- mcMoveMoleculeCoupledDLPOLY - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- mcMoveMoleculeCoupledDLPOLY - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- MCMoveMoleculeCoupledInitPert - Class in etomica.models.nitrogen
-
Standard Monte Carlo molecule-displacement trial move.
- MCMoveMoleculeCoupledInitPert(PotentialMaster, IRandom, Space, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- MCMoveMoleculeCoupledSuperBox - Class in etomica.models.nitrogen
-
Standard Monte Carlo molecule-displacement trial move for superbox.
- MCMoveMoleculeCoupledSuperBox(PotentialMaster, IRandom, Space, Box, int, int, CoordinateDefinitionNitrogenSuperBox) - Constructor for class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- MCMoveMoleculeExchange - Class in etomica.integrator.mcmove
-
Performs a trial that results in the exchange of a molecule from one box to another.
- MCMoveMoleculeExchange(PotentialMaster, IRandom, Space, IntegratorBox, IntegratorBox) - Constructor for class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- MCMoveMoleculeExchangeVLE - Class in etomica.modules.vle
-
- MCMoveMoleculeExchangeVLE(PotentialMaster, IRandom, Space, IntegratorBox, IntegratorBox) - Constructor for class etomica.modules.vle.MCMoveMoleculeExchangeVLE
-
- mcMoveMoleculeMonomer - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- MCMoveMoleculeMonomer - Class in etomica.association
-
Monte Carlo molecule-displacement trial move for monomer molecules
- MCMoveMoleculeMonomer(Simulation, PotentialMaster, Space) - Constructor for class etomica.association.MCMoveMoleculeMonomer
-
- MCMoveMoleculeMonomer(PotentialMaster, IRandom, Space, double, double) - Constructor for class etomica.association.MCMoveMoleculeMonomer
-
- mcMoveMoleculeRotate - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- MCMoveMoleculeRotateAssociated - Class in etomica.association
-
Performs a rotation of a molecule that has an orientation coordinate.
- MCMoveMoleculeRotateAssociated(PotentialMaster, IRandom, Space) - Constructor for class etomica.association.MCMoveMoleculeRotateAssociated
-
- mcMoveMoleculeSmer - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- MCMoveMoleculeSmer - Class in etomica.association
-
Monte Carlo molecule-displacement trial move for a molecule in smer
- MCMoveMoleculeSmer(Simulation, PotentialMaster, Space) - Constructor for class etomica.association.MCMoveMoleculeSmer
-
- MCMoveMoleculeSmer(PotentialMaster, IRandom, Space, double, double) - Constructor for class etomica.association.MCMoveMoleculeSmer
-
- MCMoveMultiHarmonic - Class in etomica.gaussianwork
-
MCMove which moves all atoms.
- MCMoveMultiHarmonic(P1Harmonic, IRandom) - Constructor for class etomica.gaussianwork.MCMoveMultiHarmonic
-
- MCMoveMultiHarmonic - Class in etomica.modules.multiharmonic
-
MCMove which moves all atoms.
- MCMoveMultiHarmonic(P1Harmonic, IRandom) - Constructor for class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- MCMoveOverlapListener - Class in etomica.integrator.mcmove
-
- MCMoveOverlapListener(MCMoveInsertDeleteBiased, int, double, int, double) - Constructor for class etomica.integrator.mcmove.MCMoveOverlapListener
-
- mcMoveOverlapMeter - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceAvgPressure
-
- mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceAvgPressure2
-
- mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceFE
-
- mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceFEHistogram
-
- mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceImposedFEFit
-
- mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
-
- mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceMuRoot
-
- mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceMuRoot1
-
- mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourceMuRootPMatch
-
- mcMoveOverlapMeter - Variable in class etomica.normalmode.DataSourcePMu
-
- MCMovePhaseAngle - Class in etomica.normalmode
-
- MCMovePhaseAngle(Space, NormalModesVariable, CoordinateDefinition, IRandom) - Constructor for class etomica.normalmode.MCMovePhaseAngle
-
- MCMoveReptate - Class in etomica.models.hexane
-
- MCMoveReptate(Simulation, PotentialMaster, Space) - Constructor for class etomica.models.hexane.MCMoveReptate
-
- MCMoveReptate(PotentialMaster, IRandom, double, double, boolean, Space) - Constructor for class etomica.models.hexane.MCMoveReptate
-
- mcMoveReptate - Variable in class etomica.virial.simulations.SimulationVirial
-
- mcMoveRotate - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- mcMoveRotate - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- mcMoveRotate - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- MCMoveRotate - Class in etomica.integrator.mcmove
-
Performs a rotation of an atom (not a molecule) that has an orientation coordinate.
- MCMoveRotate(PotentialMaster, IRandom, Space) - Constructor for class etomica.integrator.mcmove.MCMoveRotate
-
- mcMoveRotate - Variable in class etomica.virial.simulations.SimulationVirial
-
- mcMoveRotate - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- mcMoveRotate - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- mcMoveRotate - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- mcMoveRotate - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- MCMoveRotateAssociated - Class in etomica.association
-
Performs a rotation of an atom (not a molecule) that has an orientation coordinate.
- MCMoveRotateAssociated(PotentialMaster, IRandom, Space) - Constructor for class etomica.association.MCMoveRotateAssociated
-
- mcMoveRotateMolecule - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- mcMoveRotateMolecule - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- mcMoveRotateMolecule - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- MCMoveRotateMolecule3D - Class in etomica.integrator.mcmove
-
- MCMoveRotateMolecule3D(PotentialMaster, IRandom, Space) - Constructor for class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- MCMoveRotateMolecule3DConstraint - Class in etomica.models.nitrogen
-
MCMoveRotate that moves the molecules according to pre-set constraint angle
which is given by the parameter "angle"
This class does not consider rotational energy, so the variable "energyChange"
always returns zero
getB() always returns positive one is to ensure the proposed move is always
accepted
- MCMoveRotateMolecule3DConstraint(PotentialMaster, IRandom, Space, double, CoordinateDefinitionNitrogen, Box) - Constructor for class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- MCMoveRotateMolecule3DFixedAngle - Class in etomica.models.nitrogen
-
MCMoveRotate that moves the molecules according to pre-set constraint angle
which is given by the parameter "angle"
This class does not consider rotational energy, so the variable "energyChange"
always returns zero
getB() always returns positive one is to ensure the proposed move is always
accepted
the proposed angle criteria is based on u3 and u4 distribution
- MCMoveRotateMolecule3DFixedAngle(PotentialMaster, IRandom, Space, double, CoordinateDefinitionNitrogen, Box) - Constructor for class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- MCMoveRotateMolecule3DN2AveCosThetaConstraint - Class in etomica.models.nitrogen
-
Impose constraint to prevent the alpha-N2 phase from becoming orientationally-disordered
the constraint imposed is the average cosine theta, where
theta is the orientation angle off the molecular nominal orientation
- MCMoveRotateMolecule3DN2AveCosThetaConstraint(PotentialMaster, IRandom, Space, CoordinateDefinitionNitrogen, double) - Constructor for class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- MCMoveRotateMolecule3DSuperBox - Class in etomica.models.nitrogen
-
MC Rotate Move 3D for superbox
The potential master that being passed in this class is a "full-strength" potential without
multiplying by 0.5 for the speciesA and speciesB interaction.
- MCMoveRotateMolecule3DSuperBox(PotentialMaster, IRandom, Space, int, int, CoordinateDefinitionNitrogenSuperBox) - Constructor for class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- MCMoveRotateMoleculePhiTheta - Class in etomica.normalmode
-
- MCMoveRotateMoleculePhiTheta(PotentialMaster, IRandom, Space, Vector[], boolean) - Constructor for class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- MCMoveRotateNoSmer - Class in etomica.association
-
- MCMoveRotateNoSmer(PotentialMaster, IRandom, Space) - Constructor for class etomica.association.MCMoveRotateNoSmer
-
- mcMoves() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- MCMoveSemigrand - Class in etomica.integrator.mcmove
-
Basic Monte Carlo move for semigrand-ensemble simulations.
- MCMoveSemigrand(PotentialMaster, IRandom, Space) - Constructor for class etomica.integrator.mcmove.MCMoveSemigrand
-
- MCMoveSingleMode - Class in etomica.normalmode
-
A Monte Carlo move which selects each individual modes to move
the atoms accordingly
- MCMoveSingleMode(PotentialMaster, IRandom) - Constructor for class etomica.normalmode.MCMoveSingleMode
-
- MCMoveSmer - Class in etomica.association
-
Standard Monte Carlo atom-displacement trial move of Trimer
- MCMoveSmer(Simulation, PotentialMasterCell, Space, IPotentialAtomic) - Constructor for class etomica.association.MCMoveSmer
-
- MCMoveSmer(PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.association.MCMoveSmer
-
- mcMoveSmer - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- mcMoveSmer - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- MCMoveSmerRotate - Class in etomica.association
-
Standard Monte Carlo atom-displacement trial move.
- MCMoveSmerRotate(Simulation, PotentialMasterCell, Space, IPotentialAtomic) - Constructor for class etomica.association.MCMoveSmerRotate
-
- MCMoveSmerRotate(PotentialMasterCell, IRandom, Space, double, double, boolean, IPotentialAtomic) - Constructor for class etomica.association.MCMoveSmerRotate
-
- mcMoveSmerRotate - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- mcMoveSmerRotate - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- MCMoveSpinFlip - Class in etomica.spin
-
TODO To change the template for this generated type comment go to
Window - Preferences - Java - Code Style - Code Templates
- MCMoveSpinFlip(PotentialMaster, IRandom) - Constructor for class etomica.spin.MCMoveSpinFlip
-
- MCMoveStep - Class in etomica.integrator.mcmove
-
- MCMoveStep(PotentialMaster) - Constructor for class etomica.integrator.mcmove.MCMoveStep
-
- MCMoveStep(PotentialMaster, MCMoveStepTracker) - Constructor for class etomica.integrator.mcmove.MCMoveStep
-
- MCMoveStepDependent - Interface in etomica.integrator.mcmove
-
- MCMoveStepTracker - Class in etomica.integrator.mcmove
-
This Class tracks acceptance statistics for an MCMove and also manages the
move's step size.
- MCMoveStepTracker() - Constructor for class etomica.integrator.mcmove.MCMoveStepTracker
-
- mcMoveSwap - Variable in class etomica.freeenergy.npath.SimFe
-
- mcMoveSwap - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- mcMoveSwap - Variable in class etomica.freeenergy.npath.SimLJ
-
- MCMoveSwapCluster - Class in etomica.virial.paralleltempering
-
Swaps configurations and pairSet between boxes for a virial clustering simulation.
- MCMoveSwapCluster(IntegratorMC, IntegratorMC, Space) - Constructor for class etomica.virial.paralleltempering.MCMoveSwapCluster
-
- MCMoveSwapCluster.SwapFactory - Class in etomica.virial.paralleltempering
-
- MCMoveSwapConfiguration - Class in etomica.integrator.mcmove
-
Basic MCMove for swapping coordinates of atoms in two boxes.
- MCMoveSwapConfiguration(IntegratorBox, IntegratorBox, Space) - Constructor for class etomica.integrator.mcmove.MCMoveSwapConfiguration
-
- MCMoveSwapConfiguration.SwapFactory - Class in etomica.integrator.mcmove
-
- mcMoveTorsion - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- MCMoveTorsionAceticAcid - Class in etomica.integrator.mcmove
-
An MC Move for cluster simulations that performs torsion moves on acetic acid.
- MCMoveTorsionAceticAcid(PotentialMaster, Space, IRandom) - Constructor for class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
-
- MCMoveTracker - Class in etomica.integrator.mcmove
-
This class is responsible for tracking acceptance statistics for an MCMove.
- MCMoveTracker() - Constructor for class etomica.integrator.mcmove.MCMoveTracker
-
- mcMoveTranslate - Variable in class etomica.virial.simulations.SimulationVirial
-
- mcMoveTranslate - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- mcMoveTranslate - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- mcMoveTranslate - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- MCMoveTrialCompletedEvent - Class in etomica.integrator.mcmove
-
- MCMoveTrialCompletedEvent(MCMoveManager, boolean) - Constructor for class etomica.integrator.mcmove.MCMoveTrialCompletedEvent
-
- MCMoveTrialFailedEvent - Class in etomica.integrator.mcmove
-
MC move event that indicates the move's trial failed, meaning that
MCMove.doTrial() returned false.
- MCMoveTrialFailedEvent(MCMoveManager) - Constructor for class etomica.integrator.mcmove.MCMoveTrialFailedEvent
-
- MCMoveTrialInitiatedEvent - Class in etomica.integrator.mcmove
-
- MCMoveTrialInitiatedEvent(MCMoveManager) - Constructor for class etomica.integrator.mcmove.MCMoveTrialInitiatedEvent
-
- mcMoveVolume - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- mcMoveVolume - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- mcMoveVolume - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- mcMoveVolume - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- mcMoveVolume - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- MCMoveVolume - Class in etomica.integrator.mcmove
-
Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
- MCMoveVolume(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.mcmove.MCMoveVolume
-
- MCMoveVolume(PotentialMaster, IRandom, Space, double) - Constructor for class etomica.integrator.mcmove.MCMoveVolume
-
- mcMoveVolume - Variable in class etomica.liquidLJ.LjMd3D
-
- mcMoveVolume - Variable in class etomica.metastable.LJNPT
-
- mcMoveVolume - Variable in class etomica.modules.ensembles.LJMC
-
- mcMoveVolume - Variable in class etomica.normalmode.SimHSMDVacancy
-
- mcMoveVolume - Variable in class etomica.normalmode.SimLJVacancy
-
- mcMoveVolume - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- MCMoveVolumeAssociated - Class in etomica.association
-
Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
- MCMoveVolumeAssociated(Simulation, PotentialMaster, Space) - Constructor for class etomica.association.MCMoveVolumeAssociated
-
- MCMoveVolumeAssociated(PotentialMaster, IRandom, Space, double) - Constructor for class etomica.association.MCMoveVolumeAssociated
-
- MCMoveVolumeAssociated.Agent - Class in etomica.association
-
- MCMoveVolumeAssociatedMolecule - Class in etomica.association
-
Monte Carlo volume-change move for associating fluids simulations in the NPT ensemble.
- MCMoveVolumeAssociatedMolecule(Simulation, PotentialMaster, Space) - Constructor for class etomica.association.MCMoveVolumeAssociatedMolecule
-
- MCMoveVolumeAssociatedMolecule(Simulation, PotentialMaster, IRandom, Space, double) - Constructor for class etomica.association.MCMoveVolumeAssociatedMolecule
-
- MCMoveVolumeAssociatedMolecule.Agent - Class in etomica.association
-
- MCMoveVolumeExchange - Class in etomica.integrator.mcmove
-
Elementary Monte Carlo trial that exchanges volume between two boxs.
- MCMoveVolumeExchange(PotentialMaster, IRandom, Space, IntegratorBox, IntegratorBox) - Constructor for class etomica.integrator.mcmove.MCMoveVolumeExchange
-
- MCMoveVolumeExchangeVLE - Class in etomica.modules.vle
-
- MCMoveVolumeExchangeVLE(PotentialMaster, IRandom, Space, IntegratorBox, IntegratorBox) - Constructor for class etomica.modules.vle.MCMoveVolumeExchangeVLE
-
- MCMoveVolumeMonoclinic - Class in etomica.normalmode
-
Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
- MCMoveVolumeMonoclinic(PotentialMaster, IRandom, Space) - Constructor for class etomica.normalmode.MCMoveVolumeMonoclinic
-
- MCMoveVolumeMonoclinicAngle - Class in etomica.normalmode
-
Standard Monte Carlo volume-change move for simulations in the NPT ensemble.
- MCMoveVolumeMonoclinicAngle(PotentialMaster, IRandom, Space, Box) - Constructor for class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- MCMoveVolumeMonoclinicScaled - Class in etomica.normalmode
-
Monte Carlo volume-change move for simulations of crystalline solids in the
NPT ensemble (molecular model).
- MCMoveVolumeMonoclinicScaled(PotentialMaster, IRandom, Space, double) - Constructor for class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- MCMoveVolumeMonoclinicScaled(PotentialMaster, IRandom, Space, double, int) - Constructor for class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- MCMoveVolumeN2 - Class in etomica.models.nitrogen
-
Monte Carlo volume-change move for simulations in the NPT ensemble.
- MCMoveVolumeN2(Simulation, PotentialMaster, Space) - Constructor for class etomica.models.nitrogen.MCMoveVolumeN2
-
- MCMoveVolumeN2(PotentialMaster, IRandom, Space, double) - Constructor for class etomica.models.nitrogen.MCMoveVolumeN2
-
- MCMoveVolumeSolid - Class in etomica.normalmode
-
Monte Carlo volume-change move for simulations of crystalline solids in the
NPT ensemble.
- MCMoveVolumeSolid(PotentialMaster, CoordinateDefinition, IRandom, Space, double) - Constructor for class etomica.normalmode.MCMoveVolumeSolid
-
- MCMoveVolumeSolidNPTMolecular - Class in etomica.normalmode
-
Monte Carlo volume-change move for simulations of crystalline solids in the
NPT ensemble (molecular model).
- MCMoveVolumeSolidNPTMolecular(PotentialMaster, IRandom, Space, double) - Constructor for class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- MCMoveVolumeSolidNPTMolecular(PotentialMaster, IRandom, Space, double, int) - Constructor for class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- MCMoveVolumeSolidNPTMolecularOriented - Class in etomica.normalmode
-
Class which handles orientation of linear molecules during volume change
trials.
- MCMoveVolumeSolidNPTMolecularOriented(PotentialMaster, IRandom, Space, double, Vector[]) - Constructor for class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- mcMoveWiggle - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- mcMoveWiggle - Variable in class etomica.virial.simulations.SimulationVirial
-
- mcMoveWiggle - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- mcMoveWiggle - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- mcMoveWiggle - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- MCMoveWiggleAceticAcid - Class in etomica.integrator.mcmove
-
An MC Move for cluster simulations that "wiggles" for acetic acid.
- MCMoveWiggleAceticAcid(Simulation, PotentialMaster, Space) - Constructor for class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- MCMoveWiggleAceticAcid(PotentialMaster, IRandom, double, Space) - Constructor for class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- MCMoveWV - Class in etomica.normalmode
-
- MCMoveWV(Space, NormalModesVariable, CoordinateDefinition, IRandom) - Constructor for class etomica.normalmode.MCMoveWV
-
- mConnections - Variable in class etomica.virial.cluster.ClusterDiagram
-
- MCParacetamolMonoclinicDLMULTI - Class in etomica.paracetamol
-
Three-dimensional soft-sphere MC simulation for paracetamol molecule
using the potential model from DL_MULTI package
with inclusion of multipole ewald-summation
To get the lowest minimum configuration with MCMoveHarmonicStep
Monoclinic Crystal
The constructor takes in:
1.
- MCParacetamolMonoclinicDLMULTI(Space, int, double, int, int[]) - Constructor for class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- MCParacetamolMonoclinicDLMULTIEquilibration - Class in etomica.paracetamol
-
Three-dimensional soft-sphere MC simulation for paracetamol molecule
using the potential model from DL_MULTI package
with inclusion of multipole ewald-summation
Monoclinic Crystal
- MCParacetamolMonoclinicDLMULTIEquilibration(Space) - Constructor for class etomica.paracetamol.MCParacetamolMonoclinicDLMULTIEquilibration
-
- MCParacetamolMonoclinicDLMULTISimCalcS - Class in etomica.paracetamol
-
Three-dimensional soft-sphere MC simulation for paracetamol molecule
using the potential model from DL_MULTI package
with inclusion of multipole ewald-summation
MC simulation of Paracetamol molecules in Form I (Monoclinic) with
tabulation of the collective-coordinate S-matrix.
- MCParacetamolMonoclinicDLMULTISimCalcS(Space) - Constructor for class etomica.paracetamol.MCParacetamolMonoclinicDLMULTISimCalcS
-
- MCParacetamolOrthorhombicDLMULTI - Class in etomica.paracetamol
-
Three-dimensional soft-sphere MC simulation for paracetamol molecule
using the potential model from DL_MULTI package
with inclusion of multipole ewald-summation
Orthorhombic Crystal
* The constructor takes in:
1.
- MCParacetamolOrthorhombicDLMULTI(Space, int, double, int, int[]) - Constructor for class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- MCParacetamolOrthorhombicDLMULTIEquilibration - Class in etomica.paracetamol
-
Three-dimensional soft-sphere MC simulation for paracetamol molecule
using the potential model from DL_MULTI package
with inclusion of multipole ewald-summation
To get the lowest minimum cofiguration with MCMoveHarmonicStep
Orthorhombic Crystal
- MCParacetamolOrthorhombicDLMULTIEquilibration(Space) - Constructor for class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTIEquilibration
-
- MCParacetamolOrthorhombicDLMULTISimCalcS - Class in etomica.paracetamol
-
Three-dimensional soft-sphere MC simulation for paracetamol molecule
using the potential model from DL_MULTI package
with inclusion of multipole ewald-summation
MC simulation of Paracetamol molecules in Form II (Orthorhombic) with
tabulation of the collective-coordinate S-matrix.
- MCParacetamolOrthorhombicMoveHarmonic - Class in etomica.paracetamol
-
Three-dimensional soft-sphere MC simulation for paracetamol molecule
Orthorhombic Crystal
- MCParacetamolOrthorhombicMoveHarmonic() - Constructor for class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- MCParacetamolOrthorhombicMoveHarmonicStep - Class in etomica.paracetamol
-
Three-dimensional soft-sphere MC simulation for paracetamol molecule
Orthorhombic Crystal
- MCParacetamolOrthorhombicMoveHarmonicStep() - Constructor for class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- MCSIMULATION - Static variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- MCSIMULATION - Static variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- mcSteps - Variable in class etomica.integrator.IntegratorMD
-
- mcSteps - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- MDParacetamolMonoclinic - Class in etomica.paracetamol
-
Three-dimensional soft-sphere molecular dynamics simulation for paracetamol molecule, using
neighbor listing.
- MDParacetamolOrthorhombic - Class in etomica.paracetamol
-
Three-dimensional soft-sphere molecular dynamics simulation for paracetamol molecule, using
neighbor listing.
- ME(IData) - Method in interface etomica.data.IData
-
Minus-equals (-=) operation.
- ME(IData) - Method in class etomica.data.types.DataDouble
-
Minus-equals (-=) operation.
- ME(IData) - Method in class etomica.data.types.DataDoubleArray
-
Minus-equals (-=) operation.
- ME(IData) - Method in class etomica.data.types.DataDoubleBDArray
-
Minus-equals (-=) operation.
- ME(IData) - Method in class etomica.data.types.DataGroup
-
- ME(IData) - Method in class etomica.data.types.DataTensor
-
Minus-equals (-=) operation.
- ME(IData) - Method in class etomica.data.types.DataVector
-
Minus-equals (-=) operation.
- ME(Tensor) - Method in interface etomica.space.Tensor
-
"Minus equals" (-=) operation, subtracting the elements of the given tensor from the
respective elements of this tensor.
- ME(Vector) - Method in interface etomica.space.Vector
-
Minus-equals (-=) operation.
- ME(Tensor) - Method in class etomica.space1d.Tensor1D
-
- ME(Vector) - Method in class etomica.space1d.Vector1D
-
- ME(Tensor) - Method in class etomica.space2d.Tensor2D
-
- ME(Vector) - Method in class etomica.space2d.Vector2D
-
- ME(Tensor) - Method in class etomica.space3d.Tensor3D
-
- ME(Vector) - Method in class etomica.space3d.Vector3D
-
- ME(Tensor) - Method in class etomica.spaceNd.TensorND
-
- ME(Vector) - Method in class etomica.spaceNd.VectorND
-
- MEAM_3DMDwithGB - Class in etomica.meam
-
Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method
(MEAM) Potential.
- MEAM_3DMDwithGB() - Constructor for class etomica.meam.MEAM_3DMDwithGB
-
- MEAM_3DMDwithSnAgGB - Class in etomica.meam
-
Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method
(MEAM) Potential.
- MEAM_3DMDwithSnAgGB() - Constructor for class etomica.meam.MEAM_3DMDwithSnAgGB
-
- MEAM_3DMDwithSnCuGB - Class in etomica.meam
-
Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method
(MEAM) Potential.
- MEAM_3DMDwithSnCuGB() - Constructor for class etomica.meam.MEAM_3DMDwithSnCuGB
-
- MEAM_MC - Class in etomica.meam
-
- MEAM_MC() - Constructor for class etomica.meam.MEAM_MC
-
- MEAMMd3D - Class in etomica.meam
-
Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method
(MEAM) Potential.
- MEAMMd3D() - Constructor for class etomica.meam.MEAMMd3D
-
- MEAMMd3DforCluster - Class in etomica.meam
-
Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method
(MEAM) Potential.
- MEAMMd3DforCluster() - Constructor for class etomica.meam.MEAMMd3DforCluster
-
- MEAMMd3DThreaded - Class in etomica.threaded.domain
-
Molecular-Dynamics Simulation Using the Modified Embedded-Atom Method
(MEAM) Potential.
- MEAMMd3DThreaded(int, int) - Constructor for class etomica.threaded.domain.MEAMMd3DThreaded
-
- MEAMMd3DThreadedforCluster - Class in etomica.threaded.domain
-
- MEAMMd3DThreadedforCluster() - Constructor for class etomica.threaded.domain.MEAMMd3DThreadedforCluster
-
- measure - Static variable in class org.jmol.script.Token
-
- Measure - Class in org.jmol.util
-
- Measure() - Constructor for class org.jmol.util.Measure
-
- MEASURE_DEFAULT_FONTSIZE - Static variable in class org.jmol.viewer.JmolConstants
-
- measureallmodels - Static variable in class org.jmol.script.Token
-
- measurementlabels - Static variable in class org.jmol.script.Token
-
- measurements - Static variable in class org.jmol.script.Token
-
- measurementunits - Static variable in class org.jmol.script.Token
-
- mediaType - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Media type for which the SVG image should be rendered
- membraneDim - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- membraneDim - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- membraneThicknessPerLayer - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- membraneThicknessSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- membraneThicknessSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- membraneTotalThickness - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- membraneWidth - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- membraneWidth - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- membraneWidthSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- mERBond - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- mergeData(Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- mergeData(Map<IntSet, MeterVirialBinMultiThreaded.MyData>) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- mergeData(Map<IntSet, MeterVirialEBinMultiThreaded.MyData>) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- mergePolygonCount0 - Variable in class org.jmol.util.MeshSurface
-
- mergeVertexCount0 - Variable in class org.jmol.util.MeshSurface
-
- mesh - Static variable in class org.jmol.script.Token
-
- meshRibbon - Static variable in class org.jmol.script.Token
-
- meshscale - Static variable in class org.jmol.script.Token
-
- MeshSurface - Class in org.jmol.util
-
- MeshSurface() - Constructor for class org.jmol.util.MeshSurface
-
- meshType - Variable in class org.jmol.util.MeshSurface
-
- MESSAGE_ABOUT_TO_TRANSCODE - Static variable in class etomica.graph.view.rasterizer.Main
-
- MESSAGE_ABOUT_TO_TRANSCODE_SOURCE - Static variable in class etomica.graph.view.rasterizer.Main
-
- MESSAGE_CONVERSION_FAILED - Static variable in class etomica.graph.view.rasterizer.Main
-
- MESSAGE_CONVERSION_SUCCESS - Static variable in class etomica.graph.view.rasterizer.Main
-
- Messages - Class in etomica.graph.view.rasterizer
-
This class manages the message for the bridge module.
- Messages() - Constructor for class etomica.graph.view.rasterizer.Messages
-
This class does not need to be instantiated.
- messagestylechime - Static variable in class org.jmol.script.Token
-
- Metadata - Interface in etomica.graph.model
-
- metaDataComparator - Static variable in class etomica.graph.model.impl.MetadataImpl
-
- MetadataImpl - Class in etomica.graph.model.impl
-
- MetadataImpl(char, char) - Constructor for class etomica.graph.model.impl.MetadataImpl
-
- meter - Variable in class etomica.data.meter.MeterProfile
-
Meter that defines the property being profiled.
- meter - Variable in class etomica.data.meter.MeterProfileByAtoms
-
Meter that defines the property being profiled.
- meter - Variable in class etomica.data.meter.MeterProfileByVolume
-
Meter that defines the property being profiled.
- meter - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- meter - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- meter - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- meter - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- meter - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- meter - Variable in class etomica.modules.droplet.AtomFilterLiquid
-
- meter - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
-
- meter - Variable in class etomica.normalmode.HTTPSoftSphereApplet
-
- meter - Variable in class etomica.normalmode.SimOverlapLJModule.MeterPotentialEnergyDifference
-
- meter - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- meter - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- meter - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- meter - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- meter - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- meter - Variable in class etomica.spin.Heisenberg
-
- Meter - Class in etomica.units
-
The meter unit of length, equal to 10^10 angstroms.
- meter - Variable in class etomica.virial.simulations.SimulationVirial
-
- meter - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- meter - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- meterA - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- meterA - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- meterA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
-
- MeterAPIPotentialEnergy - Class in etomica.normalmode
-
Meter that returns the potential energy using an IAPIPotential.
- MeterAPIPotentialEnergy(IAPIPotential) - Constructor for class etomica.normalmode.MeterAPIPotentialEnergy
-
- MeterAtomicDisplacement - Class in etomica.normalmode
-
Calculates the average atomic displacement from their lattice sites
- MeterAtomicDisplacement(Space, CoordinateDefinition) - Constructor for class etomica.normalmode.MeterAtomicDisplacement
-
- MeterAvgBondLength - Class in etomica.data.meter
-
- MeterAvgBondLength() - Constructor for class etomica.data.meter.MeterAvgBondLength
-
- meterB - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- meterB - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- meterB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceFE
-
- MeterBoltzmann - Class in etomica.models.nitrogen
-
Meter used for overlap sampling in the target-sampled system.
- MeterBoltzmann(IntegratorBox, MeterPotentialEnergy) - Constructor for class etomica.models.nitrogen.MeterBoltzmann
-
- MeterBoltzmann - Class in etomica.normalmode
-
Meter used for overlap sampling in the target-sampled system.
- MeterBoltzmann(IntegratorBox, MeterPotentialEnergy, double, double) - Constructor for class etomica.normalmode.MeterBoltzmann
-
- MeterBoltzmannA - Class in etomica.gaussianwork
-
Multiharmonic system
Meter used for overlap sampling in the A-sampled system.
- MeterBoltzmannA(IntegratorBox, PotentialMaster) - Constructor for class etomica.gaussianwork.MeterBoltzmannA
-
- MeterBoltzmannB - Class in etomica.gaussianwork
-
Multiharmonic system
Meter used for overlap sampling in the B-sampled system.
- MeterBoltzmannB(IntegratorBox, PotentialMaster) - Constructor for class etomica.gaussianwork.MeterBoltzmannB
-
- MeterBoltzmannDirect - Class in etomica.models.nitrogen
-
Meter used for overlap sampling in the target-sampled system.
- MeterBoltzmannDirect(IntegratorBox, MeterPotentialEnergy) - Constructor for class etomica.models.nitrogen.MeterBoltzmannDirect
-
- MeterBoltzmannHarmonic - Class in etomica.normalmode
-
Meter used for overlap sampling in the harmonic-sampled system.
- MeterBoltzmannHarmonic(MCMoveHarmonic, PotentialMaster) - Constructor for class etomica.normalmode.MeterBoltzmannHarmonic
-
- MeterBoltzmannHTTP - Class in etomica.normalmode
-
Same as TargetTP class but is used by MethodBoltzmannHTTP
It is to illustrate the idea of HTTP method.
- MeterBoltzmannHTTP(PotentialMaster, ISpecies, Space, Simulation) - Constructor for class etomica.normalmode.MeterBoltzmannHTTP
-
- MeterBoltzmannRotPerturb - Class in etomica.models.nitrogen
-
Meter used for overlap sampling in the target-sampled system.
- MeterBoltzmannRotPerturb(IntegratorMC, PotentialMaster, ISpecies, Space, Simulation, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- MeterBoltzmannTarget - Class in etomica.normalmode
-
Meter used for overlap sampling in the target-sampled system.
- MeterBoltzmannTarget(DataSourceScalar, DataSourceScalar) - Constructor for class etomica.normalmode.MeterBoltzmannTarget
-
- MeterChainLength - Class in etomica.modules.chainequilibrium
-
- MeterChainLength(AtomLeafAgentManager<IAtom[]>) - Constructor for class etomica.modules.chainequilibrium.MeterChainLength
-
- MeterChainLength.AtomTag - Class in etomica.modules.chainequilibrium
-
- MeterCompareMultipleWVBrute - Class in etomica.models.oneDHardRods
-
Meter which measures a hard rod energy plus a harmonic energy of a system
The harmonic energy is determined by removing the effects of some
normal mode coordinates, and applying 1/2 omega^2 nmc^2 to them.
- MeterCompareMultipleWVBrute(PotentialMaster, CoordinateDefinition, Box) - Constructor for class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- MeterCompareMultipleWVBrute(String, PotentialMaster, CoordinateDefinition, Box) - Constructor for class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- MeterCompareWVShortcut - Class in etomica.models.oneDHardRods
-
This meter assumes the use of only MCMoveCompareMode in the simulation.
- MeterCompareWVShortcut(PotentialMaster, MCMoveCompareMultipleWV) - Constructor for class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- MeterConversion - Class in etomica.modules.chainequilibrium
-
Meter for the reaction conversion (fraction of reacted sites).
- MeterConversion(Box, AtomLeafAgentManager) - Constructor for class etomica.modules.chainequilibrium.MeterConversion
-
- meterCountAtoms - Variable in class etomica.modules.adsorption.ModifierPMu
-
- meterCycles - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- meterCycles - Variable in class etomica.simulation.prototypes.HSMC2D
-
- meterCycles - Variable in class etomica.simulation.prototypes.SoftSphere3d
-
- MeterDADB - Class in etomica.normalmode
-
- MeterDADB(Space, DataSourceScalar, PotentialMaster, CoordinateDefinition, double) - Constructor for class etomica.normalmode.MeterDADB
-
- MeterDDP - Class in etomica.normalmode
-
Meter that measures the overlap averages for perturbing from a solid at one
density into other densities.
- MeterDDP(PotentialMaster, ISpecies, Space, Simulation) - Constructor for class etomica.normalmode.MeterDDP
-
- meterDeformation - Variable in class etomica.modules.droplet.Droplet
-
- MeterDeformation - Class in etomica.modules.droplet
-
- MeterDeformation(Space) - Constructor for class etomica.modules.droplet.MeterDeformation
-
- MeterDensity - Class in etomica.data.meter
-
Meter for measurement of the total molecule number density in a box
Molecule number density is defined (number of molecules)/(volume of box)
- MeterDensity(Space) - Constructor for class etomica.data.meter.MeterDensity
-
- meterDensity - Variable in class etomica.modules.vle.MCMoveMoleculeExchangeVLE
-
- meterDensity - Variable in class etomica.modules.vle.MCMoveVolumeExchangeVLE
-
- MeterDensityCO - Class in etomica.modules.catalysis
-
- MeterDensityCO(Box, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.MeterDensityCO
-
- MeterDensityCO2 - Class in etomica.modules.catalysis
-
- MeterDensityCO2(Box, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.MeterDensityCO2
-
- MeterDensityDistribution - Class in etomica.metastable
-
- MeterDensityDistribution(Space, Box, int) - Constructor for class etomica.metastable.MeterDensityDistribution
-
- MeterDensityO2 - Class in etomica.modules.catalysis
-
- MeterDensityO2(Box, ISpecies, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.MeterDensityO2
-
- MeterDensitySides - Class in etomica.modules.mu
-
- MeterDensitySides(Box, ISpecies, boolean) - Constructor for class etomica.modules.mu.MeterDensitySides
-
- MeterDifferentImageAdd - Class in etomica.models.oneDHardRods
-
Uses a Widom-like insertion of a mode to calculate a probability.
- MeterDifferentImageAdd(Simulation, Space, double, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- MeterDifferentImageAdd(Simulation, Space, double, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes, String) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- MeterDifferentImageAdd1D - Class in etomica.models.oneDHardRods
-
Uses a Widom-like insertion of a mode to calculate a probability.
- MeterDifferentImageAdd1D(String, int, double, Simulation, Primitive, Basis, CoordinateDefinition, NormalModes, double) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
-
- MeterDifferentImageAddDoubleSize - Class in etomica.models.oneDHardRods
-
Uses a Widom-like insertion of a mode to calculate a probability.
- MeterDifferentImageAddDoubleSize(Simulation, Space, double, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageAddDoubleSize
-
- MeterDifferentImageAddDoubleSize(Simulation, Space, double, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes, String) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageAddDoubleSize
-
- MeterDifferentImageSubtract - Class in etomica.models.oneDHardRods
-
Uses a Widom-like insertion of a mode to calculate a probability.
- MeterDifferentImageSubtract(Simulation, Space, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- MeterDifferentImageSubtract(Simulation, Space, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes, String) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- MeterDifferentImageSubtract1D - Class in etomica.models.oneDHardRods
-
Uses a Widom-like insertion of a mode to calculate a probability.
- MeterDifferentImageSubtract1D(String, int, double, Simulation, Primitive, Basis, CoordinateDefinition, NormalModes, double) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
-
- MeterDifferentImageSubtractDoubleSize - Class in etomica.models.oneDHardRods
-
Uses a Widom-like insertion of a mode to calculate a probability.
- MeterDifferentImageSubtractDoubleSize(Simulation, Space, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageSubtractDoubleSize
-
- MeterDifferentImageSubtractDoubleSize(Simulation, Space, CoordinateDefinition, NormalModes, CoordinateDefinition, PotentialMasterList, int[], NormalModes, String) - Constructor for class etomica.models.oneDHardRods.MeterDifferentImageSubtractDoubleSize
-
- MeterDihedralAngle - Class in etomica.data.meter
-
Meter for tabulation of a dihedral angle distribution between nearest neighbors.
- MeterDihedralAngle(Space) - Constructor for class etomica.data.meter.MeterDihedralAngle
-
Creates meter with default to compute dihedral angle for all
leaf atoms in a box.
- MeterDimerFraction - Class in etomica.modules.reactionequilibrium
-
- MeterDimerFraction(AtomLeafAgentManager) - Constructor for class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- meterDimerFraction - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- MeterDimerMoleFraction - Class in etomica.association
-
Meter for measurement of species mole fraction within a specified subvolume
- MeterDimerMoleFraction(Space, Box) - Constructor for class etomica.association.MeterDimerMoleFraction
-
- MeterDipoleSumSquared1site - Class in etomica.data.meter
-
meter for (sum dipole)^2, used for dielectric constant calculation
- MeterDipoleSumSquared1site(Space, Box, double) - Constructor for class etomica.data.meter.MeterDipoleSumSquared1site
-
- MeterDipoleSumSquaredMappedAverage - Class in etomica.data.meter
-
meter for AEE use mapping average
- MeterDipoleSumSquaredMappedAverage(Space, Box, Simulation, double, double, PotentialMaster) - Constructor for class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- MeterDipoleSumSquaredTIP4PWater - Class in etomica.data.meter
-
meter for (sum dipole)^2
used for dielectric constant calculation
- MeterDipoleSumSquaredTIP4PWater(Space, Box) - Constructor for class etomica.data.meter.MeterDipoleSumSquaredTIP4PWater
-
- MeterDirectInitPert - Class in etomica.models.nitrogen
-
Meter used for overlap sampling in the target-sampled system.
- MeterDirectInitPert(IntegratorBox, MeterPotentialEnergy, CoordinateDefinitionNitrogen, IRandom) - Constructor for class etomica.models.nitrogen.MeterDirectInitPert
-
- MeterDirectSamplingHarmonic - Class in etomica.normalmode
-
Meter used for overlap sampling in the harmonic-sampled system.
- MeterDirectSamplingHarmonic(MCMoveHarmonic, PotentialMaster) - Constructor for class etomica.normalmode.MeterDirectSamplingHarmonic
-
- MeterDirectSamplingTarget - Class in etomica.normalmode
-
Meter used for overlap sampling in the target-sampled system.
- MeterDirectSamplingTarget(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterDirectSamplingTarget
-
- MeterDisplacementMoleculeRMS - Class in etomica.normalmode
-
- MeterDisplacementMoleculeRMS(Space, CoordinateDefinitionMolecule) - Constructor for class etomica.normalmode.MeterDisplacementMoleculeRMS
-
- MeterDisplacementRMS - Class in etomica.normalmode
-
- MeterDisplacementRMS(Space, CoordinateDefinition) - Constructor for class etomica.normalmode.MeterDisplacementRMS
-
- MeterDP - Class in etomica.normalmode
-
Meter that measures the overlap averages for perturbing from a solid at one
density into other densities.
- MeterDP(PotentialMaster, ISpecies, Space, Simulation) - Constructor for class etomica.normalmode.MeterDP
-
- meterE2E - Variable in class etomica.modules.colloid.ColloidGraphic
-
- MeterElongation - Class in etomica.modules.materialfracture
-
- MeterElongation() - Constructor for class etomica.modules.materialfracture.MeterElongation
-
- MeterEnd2End - Class in etomica.modules.colloid
-
Measures the end-to-end squared distance for the colloid system, averaged
across the grafted chains.
- MeterEnd2End(Space) - Constructor for class etomica.modules.colloid.MeterEnd2End
-
- MeterEndToEnd - Class in etomica.modules.rheology
-
Meter that measures that end to end distance of the molecules
- MeterEndToEnd(Space) - Constructor for class etomica.modules.rheology.MeterEndToEnd
-
- meterEnergy - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
-
- meterEnergy - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- MeterEnergy - Class in etomica.data.meter
-
Meter for measurement of the total (potential and kinetic) energy in a box
This meter is constructed from kinetic-energy and a potential-energy meters
An instance of this meter is placed in each box to allow for energy measurements in the box
- MeterEnergy(PotentialMaster, Box) - Constructor for class etomica.data.meter.MeterEnergy
-
- meterEnergy - Variable in class etomica.models.nitrogen.MeterBoltzmann
-
- meterEnergy - Variable in class etomica.models.nitrogen.MeterBoltzmannDirect
-
- meterEnergy - Variable in class etomica.models.nitrogen.MeterDirectInitPert
-
- meterEnergy - Variable in class etomica.normalmode.MeterBoltzmann
-
- meterEnergy - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
-
- meterEnergy - Variable in class etomica.normalmode.MeterBoltzmannTarget
-
- meterEnergy - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- meterEnergy - Variable in class etomica.normalmode.MeterDirectSamplingTarget
-
- meterEnergy - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
-
- meterEnergy - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- meterEnergy - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- meterEnergy - Variable in class etomica.normalmode.MeterWorkTargetBennet
-
- meterEnergy - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- meterEnergy - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- meterEnergy - Variable in class etomica.normalmode.SimUmbrella
-
- meterEnergy - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- meterEnergy - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
-
- meterEnergyA - Variable in class etomica.gaussianwork.MeterBoltzmannA
-
- meterEnergyA - Variable in class etomica.gaussianwork.MeterBoltzmannB
-
- meterEnergyB - Variable in class etomica.gaussianwork.MeterBoltzmannA
-
- meterEnergyB - Variable in class etomica.gaussianwork.MeterBoltzmannB
-
- MeterEnthalpy(IntegratorGear4NPH, int) - Constructor for class etomica.integrator.IntegratorGear4NPH.MeterEnthalpy
-
- MeterEntropy - Class in etomica.modules.entropylottery
-
Calculates the entropy of the distribution of Atoms in a Box
using Stirling's approximation.
- MeterEntropy() - Constructor for class etomica.modules.entropylottery.MeterEntropy
-
- MeterExcessAdsorbed - Class in etomica.modules.adsorption
-
- MeterExcessAdsorbed(ISpecies, EOSSW) - Constructor for class etomica.modules.adsorption.MeterExcessAdsorbed
-
- MeterF - Class in etomica.models.oneDHardRods
-
- MeterF(CoordinateDefinition) - Constructor for class etomica.models.oneDHardRods.MeterF
-
- MeterFlux - Class in etomica.modules.dcvgcmd
-
- MeterFlux(MyMCMove, IntegratorDCVGCMD) - Constructor for class etomica.modules.dcvgcmd.MeterFlux
-
- MeterFlux - Class in etomica.modules.rosmosis
-
Meter to measure flux across a boundary or boundaries.
- MeterFlux(Simulation, Space) - Constructor for class etomica.modules.rosmosis.MeterFlux
-
- meterFlux0 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- meterFlux1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- meterFlux2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- meterFlux3 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- MeterFreeEnergy - Class in etomica.modules.multiharmonic
-
Computes the free-enery difference through free-energy perturbation.
- MeterFreeEnergy(P1Harmonic, P1Harmonic) - Constructor for class etomica.modules.multiharmonic.MeterFreeEnergy
-
- meterHarm - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- meterHarm - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- meterHarmonic - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
-
- meterHarmonic - Variable in class etomica.normalmode.MeterWorkBennetTarget
-
- meterHarmonic - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- meterHarmonic - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
-
- MeterHarmonicCoordinate - Class in etomica.normalmode
-
- MeterHarmonicCoordinate(CoordinateDefinition) - Constructor for class etomica.normalmode.MeterHarmonicCoordinate
-
- meterHarmonicCoordinate - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- meterHarmonicEnergy - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- meterHarmonicEnergy - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.MeterDirectSamplingTarget
-
- MeterHarmonicEnergy - Class in etomica.normalmode
-
Meter that calculates the harmonic energy of a configuration given
eigenvectors and omegas corresponding to wave vectors.
- MeterHarmonicEnergy(CoordinateDefinition, NormalModes) - Constructor for class etomica.normalmode.MeterHarmonicEnergy
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.MeterWorkTargetBennet
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.SimBennet
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.SimOverlap
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.SimTargetUmbrella
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.SimUmbrella
-
- meterHarmonicEnergy - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- MeterHarmonicEnergyFromMove - Class in etomica.normalmode
-
Meter that returns the harmonic energy from the MC move as a data source.
- MeterHarmonicEnergyFromMove(MCMoveHarmonic) - Constructor for class etomica.normalmode.MeterHarmonicEnergyFromMove
-
- MeterHarmonicSingleEnergy - Class in etomica.normalmode
-
Meter that calculates the Boltzmann-factored harmonic energy of each normal mode for a
configuration given eigenvectors and omegas corresponding to wave vectors.
- MeterHarmonicSingleEnergy(CoordinateDefinition, NormalModes) - Constructor for class etomica.normalmode.MeterHarmonicSingleEnergy
-
- MeterHyperVirial - Class in etomica.data.meter
-
Meter for measurement of the hypervirial, r^2 d2u/dr2 + r du/dr
- MeterHyperVirial() - Constructor for class etomica.data.meter.MeterHyperVirial
-
- MeterHyperVirial(Space, boolean) - Constructor for class etomica.data.meter.MeterHyperVirial
-
If full is true, then the pressure is also calculated and three values
are returned.
- meterJacobian - Variable in class etomica.normalmode.MCMovePhaseAngle
-
- meterJacobian - Variable in class etomica.normalmode.MCMoveWV
-
- MeterJacobian - Class in etomica.normalmode
-
- MeterJacobian(CoordinateDefinition, NormalModesVariable) - Constructor for class etomica.normalmode.MeterJacobian
-
- meterKE - Variable in class etomica.data.meter.MeterTemperature
-
- meterKE - Variable in class etomica.integrator.IntegratorMD
-
- MeterKineticEnergy - Class in etomica.data.meter
-
Meter for the total kinetic energy in a box
Computes total KE by summing values of KE returned by every atom in the box.
- MeterKineticEnergy() - Constructor for class etomica.data.meter.MeterKineticEnergy
-
- MeterKineticEnergyFromIntegrator - Class in etomica.data.meter
-
Acts as a DataSource to retrieve the energy from the integrator
- MeterKineticEnergyFromIntegrator() - Constructor for class etomica.data.meter.MeterKineticEnergyFromIntegrator
-
- MeterKineticEnergyFromIntegrator(IntegratorMD) - Constructor for class etomica.data.meter.MeterKineticEnergyFromIntegrator
-
- MeterKineticEnergyRigid - Class in etomica.data.meter
-
Meter for the total kinetic energy in a box
Computes total KE by summing values of KE returned by every atom in the box.
- MeterKineticEnergyRigid(Space, Simulation) - Constructor for class etomica.data.meter.MeterKineticEnergyRigid
-
- MeterKineticEnergyRigid(Space, Simulation, Box) - Constructor for class etomica.data.meter.MeterKineticEnergyRigid
-
- MeterLoad - Class in etomica.modules.materialfracture
-
Meter that calculates the stress within the gage cell.
- MeterLoad(PotentialCalculationForceStress) - Constructor for class etomica.modules.materialfracture.MeterLoad
-
- MeterLocalDensity - Class in etomica.data.meter
-
Meter for measurement of density within a specified subvolume
- MeterLocalDensity(Box) - Constructor for class etomica.data.meter.MeterLocalDensity
-
- MeterLocalMoleFraction - Class in etomica.data.meter
-
Meter for measurement of species mole fraction within a specified subvolume
- MeterLocalMoleFraction(Space, Box) - Constructor for class etomica.data.meter.MeterLocalMoleFraction
-
- MeterMappedRdf - Class in etomica.mappedRdf
-
Created by aksharag on 5/16/17.
- MeterMappedRdf(Space) - Constructor for class etomica.mappedRdf.MeterMappedRdf
-
- MeterMappedU - Class in etomica.mappedvirial
-
- MeterMappedU(Space, PotentialMaster, Box, int) - Constructor for class etomica.mappedvirial.MeterMappedU
-
- MeterMappedVirial - Class in etomica.mappedvirial
-
- MeterMappedVirial(Space, PotentialMaster, Box, int) - Constructor for class etomica.mappedvirial.MeterMappedVirial
-
- MeterMappedVirialV - Class in etomica.mappedvirial
-
- MeterMappedVirialV(Space, PotentialMaster, Box, int) - Constructor for class etomica.mappedvirial.MeterMappedVirialV
-
- MeterMaxExpansion - Class in etomica.normalmode
-
measures the maximum amount by which by which the HS diameter could increase
without causing overlap
- MeterMaxExpansion(Space, Box, NeighborListManager) - Constructor for class etomica.normalmode.MeterMaxExpansion
-
- MeterMBAR - Class in etomica.modules.multiharmonic.mbar
-
- MeterMBAR(DataSourceScalar[], double) - Constructor for class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- MeterMeanForce - Class in etomica.mappedvirial
-
- MeterMeanForce(Space, PotentialMaster, Potential2SoftSpherical, Box, int) - Constructor for class etomica.mappedvirial.MeterMeanForce
-
- MeterMeanSquareDisplacement - Class in etomica.data.meter
-
Computes the mean square displacement for a set of atoms.
- MeterMeanSquareDisplacement(Space, IntegratorBox) - Constructor for class etomica.data.meter.MeterMeanSquareDisplacement
-
- MeterMeanSquareDisplacement(Space, IntegratorBox, AtomIteratorBoxDependent) - Constructor for class etomica.data.meter.MeterMeanSquareDisplacement
-
- MeterMoleFraction - Class in etomica.data.meter
-
Meter for measurement of the species mole fraction in a box.
- MeterMoleFraction() - Constructor for class etomica.data.meter.MeterMoleFraction
-
- MeterMomentumCOM - Class in etomica.data.meter
-
Returns the instantaneous total center-of-mass momentum, summed over all
leaf atoms in a box.
- MeterMomentumCOM(Space) - Constructor for class etomica.data.meter.MeterMomentumCOM
-
- MeterNMCBaskets - Class in etomica.models.oneDHardRods
-
- MeterNMCBaskets(CoordinateDefinition, Vector[], int) - Constructor for class etomica.models.oneDHardRods.MeterNMCBaskets
-
- MeterNMCBaskets(CoordinateDefinition, Vector[], int, boolean) - Constructor for class etomica.models.oneDHardRods.MeterNMCBaskets
-
- MeterNMolecules - Class in etomica.data.meter
-
Meter for recording the total number of molecules in the box
- MeterNMolecules() - Constructor for class etomica.data.meter.MeterNMolecules
-
- MeterNormalizedCoord - Class in etomica.models.nitrogen
-
Sample the distribution of the normalized coordinate for the atoms/ molecules
from coordinate definition, calcU method.
- MeterNormalizedCoord(Box, CoordinateDefinition, ISpecies) - Constructor for class etomica.models.nitrogen.MeterNormalizedCoord
-
- MeterNormalizedCoord(Box, CoordinateDefinition, ISpecies, boolean) - Constructor for class etomica.models.nitrogen.MeterNormalizedCoord
-
- MeterNormalizedCoordBeta - Class in etomica.models.nitrogen
-
Sample the distribution of the normalized coordinate for the atoms/ molecules
from coordinate definition, calcU method.
- MeterNormalizedCoordBeta(Box, CoordinateDefinition, ISpecies) - Constructor for class etomica.models.nitrogen.MeterNormalizedCoordBeta
-
- MeterNormalMode - Class in etomica.normalmode
-
Calculates the S-matrix for a configuration.
- MeterNormalMode() - Constructor for class etomica.normalmode.MeterNormalMode
-
- meterNormalMode - Variable in class etomica.normalmode.WriteS
-
- MeterNormalModeCoordinate - Class in etomica.models.oneDHardRods
-
Class which calculates all of the normal mode coordinates for a system.
- MeterNormalModeCoordinate(CoordinateDefinition, Vector[]) - Constructor for class etomica.models.oneDHardRods.MeterNormalModeCoordinate
-
- MeterNormalStress - Class in etomica.modules.rheology
-
Meter to measure normal stress of a polymer in a shear field.
- MeterNormalStress(Space) - Constructor for class etomica.modules.rheology.MeterNormalStress
-
- MeterOrientation - Class in etomica.modules.interfacial
-
Meter for collecting the molecular orientation of the dimer.
- MeterOrientation(Space) - Constructor for class etomica.modules.interfacial.MeterOrientation
-
- MeterOrientationDistribution - Class in etomica.models.nitrogen
-
Meter that measures the spherical coordinate angles
angle[0]: is theta, angle between the projection vector (molecular axis vector onto xy plane)
and x-axis
angle[1]: is phi, angle between the molecular axis vector and z-axis
- MeterOrientationDistribution(Box, CoordinateDefinitionNitrogen, ISpecies) - Constructor for class etomica.models.nitrogen.MeterOrientationDistribution
-
- MeterOrientationOrderParameter - Class in etomica.models.nitrogen
-
Meter used to sample orientation order parameter
- MeterOrientationOrderParameter(CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.MeterOrientationOrderParameter
-
- MeterOsmoticPressure - Class in etomica.modules.osmosis
-
Osmotic pressure meter that calculates the difference in
- MeterOsmoticPressure(Space, P1HardBoundary[]) - Constructor for class etomica.modules.osmosis.MeterOsmoticPressure
-
- MeterOsmoticPressure - Class in etomica.modules.rosmosis
-
Meter to measure flux across a boundary or boundaries.
- MeterOsmoticPressure(IPotentialCalculationWallForce, Box) - Constructor for class etomica.modules.rosmosis.MeterOsmoticPressure
-
- MeterOverlap - Class in etomica.models.oneDHardRods
-
- MeterOverlap(String, Dimension, DataSourceScalar, DataSourceScalar, double) - Constructor for class etomica.models.oneDHardRods.MeterOverlap
-
Put the system you are measuring in as the first DataSourceScalar
- MeterOverlap - Class in etomica.overlap
-
- MeterOverlap(IDataSource, IDataSource, double, boolean) - Constructor for class etomica.overlap.MeterOverlap
-
Meter to measure the "overlap" function for free energy calculations,
used as input to an AccumulatorVirialOverlapSingleAverage.
- meterOverlapA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- meterOverlapA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- meterOverlapB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- meterOverlapB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- MeterOverlapSameGaussian - Class in etomica.models.oneDHardRods
-
- MeterOverlapSameGaussian(String, Dimension, DataSourceScalar, DataSourceScalar, double) - Constructor for class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
Put the system you are measuring in as the first DataSourceScalar
- MeterOverlapSameGaussian1D - Class in etomica.models.oneDHardRods
-
- MeterOverlapSameGaussian1D(String, Dimension, DataSourceScalar, DataSourceScalar, double) - Constructor for class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D
-
Put the system you are measuring in as the first DataSourceScalar
- MeterOverlapSwitch - Class in etomica.normalmode
-
Meter whose purpose in life is to measure the overlap between systems
defined by a combination of two energy meters.
- MeterOverlapSwitch(PotentialMaster, PotentialMaster) - Constructor for class etomica.normalmode.MeterOverlapSwitch
-
- meterPE - Variable in class etomica.integrator.IntegratorBox
-
- meterPE - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- meterPE - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- meterPE - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- meterPE - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- meterPE - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- meterPE - Static variable in class etomica.models.rowley.DimerApproach
-
- meterPE - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- meterPE - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- meterPE - Variable in class etomica.normalmode.MeterDADB
-
- meterPE - Variable in class etomica.normalmode.MeterSolidProps
-
- meterPE - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- meterPE - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- meterPE - Variable in class etomica.virial.ClusterSumExternalField
-
- meterPE - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- meterPE1 - Variable in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- meterPE1 - Variable in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- meterPE1 - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- meterPE1 - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- meterPE2 - Variable in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- meterPE2 - Variable in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- meterPE2 - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- meterPE2 - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- MeterPhiDeviation - Class in etomica.normalmode
-
Meter that measures the average tilt angle (not the angle of average tilt!)
- MeterPhiDeviation(Space) - Constructor for class etomica.normalmode.MeterPhiDeviation
-
- MeterPlaneSlip - Class in etomica.normalmode
-
Meter that measures the average tilt angle (not the angle of average tilt!)
- MeterPlaneSlip(Space, ISpecies, int, int, int) - Constructor for class etomica.normalmode.MeterPlaneSlip
-
- MeterPositionCOM - Class in etomica.data.meter
-
Returns the instantaneous center-of-mass position, summed over all
leaf atoms in a box, dividing by the number of atoms.
- MeterPositionCOM(Space) - Constructor for class etomica.data.meter.MeterPositionCOM
-
- meterPotential - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- meterPotential - Variable in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- meterPotential - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- meterPotential - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- meterPotential - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- meterPotential - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- meterPotential - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- meterPotential - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- meterPotential - Variable in class etomica.normalmode.MeterDDP
-
- meterPotential - Variable in class etomica.normalmode.MeterDP
-
- meterPotential - Variable in class etomica.normalmode.MeterTargetTP
-
- MeterPotentialEnergy - Class in etomica.data.meter
-
Meter for evaluation of the potential energy in a box.
- MeterPotentialEnergy(PotentialMaster) - Constructor for class etomica.data.meter.MeterPotentialEnergy
-
- meterPotentialEnergy - Variable in class etomica.models.nitrogen.MeterBoltzmann
-
- meterPotentialEnergy - Variable in class etomica.models.nitrogen.MeterBoltzmannDirect
-
- meterPotentialEnergy - Variable in class etomica.models.nitrogen.MeterDirectInitPert
-
- meterPotentialEnergy - Variable in class etomica.normalmode.MeterBoltzmann
-
- MeterPotentialEnergyComposite(PotentialMaster, PotentialMaster, double, int) - Constructor for class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- MeterPotentialEnergyComposite(PotentialMaster, PotentialMaster, double, int) - Constructor for class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- MeterPotentialEnergyComposite(PotentialMaster, PotentialMaster, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- MeterPotentialEnergyComposite(PotentialMaster, PotentialMaster, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- MeterPotentialEnergyCutoff - Class in etomica.liquidLJ
-
Meter for evaluation of the potential energy in a box.
- MeterPotentialEnergyCutoff(PotentialMaster, Space, double[]) - Constructor for class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- MeterPotentialEnergyDifference(DataSourceScalar, double) - Constructor for class etomica.normalmode.SimOverlapLJModule.MeterPotentialEnergyDifference
-
- MeterPotentialEnergyFromIntegrator - Class in etomica.data.meter
-
Acts as a DataSource to retrieve the energy from the integrator
- MeterPotentialEnergyFromIntegrator() - Constructor for class etomica.data.meter.MeterPotentialEnergyFromIntegrator
-
- MeterPotentialEnergyFromIntegrator(IntegratorBox) - Constructor for class etomica.data.meter.MeterPotentialEnergyFromIntegrator
-
- meterPotentialMeasured - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- meterPotentialMeasured - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- meterPotentialSampled - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- meterPotentialSampled - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- MeterPressure - Class in etomica.data.meter
-
Meter for evaluation of the soft-potential pressure in a box.
- MeterPressure(Space) - Constructor for class etomica.data.meter.MeterPressure
-
- meterPressure - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- MeterPressure2 - Class in etomica.modules.vle
-
Meter for evaluation of the soft-potential pressure in a box.
- MeterPressure2(Space) - Constructor for class etomica.modules.vle.MeterPressure2
-
- MeterPressureByVolumeChange - Class in etomica.data.meter
-
Evaluates the pressure by examining the change in energy accompanying
small changes in volume.
- MeterPressureByVolumeChange(Space) - Constructor for class etomica.data.meter.MeterPressureByVolumeChange
-
- MeterPressureByVolumeChange(Space, boolean[]) - Constructor for class etomica.data.meter.MeterPressureByVolumeChange
-
- MeterPressureByVolumeChange(Space, BoxInflateDeformable) - Constructor for class etomica.data.meter.MeterPressureByVolumeChange
-
- MeterPressureByVolumeChange(Space, boolean[], BoxInflateDeformable) - Constructor for class etomica.data.meter.MeterPressureByVolumeChange
-
- MeterPressureByVolumeChange.DataSourceExp - Class in etomica.data.meter
-
Transforms the scaling from linear (-s to +s) to exponential (exp(-s) to exp(+s))
- MeterPressureHard - Class in etomica.data.meter
-
Meter for the pressure (given as the compressibility factor) of a hard potential.
- MeterPressureHard(Space) - Constructor for class etomica.data.meter.MeterPressureHard
-
- MeterPressureHardTensor - Class in etomica.data.meter
-
- MeterPressureHardTensor(Space) - Constructor for class etomica.data.meter.MeterPressureHardTensor
-
- MeterPressureMolecular - Class in etomica.data.meter
-
Meter for evaluation of the soft-potential (molecular) pressure in a box.
- MeterPressureMolecular(Space) - Constructor for class etomica.data.meter.MeterPressureMolecular
-
- MeterPressureSuperBox - Class in etomica.normalmode
-
Meter for evaluation of the soft-potential pressure in a box.
- MeterPressureSuperBox(Space) - Constructor for class etomica.normalmode.MeterPressureSuperBox
-
- MeterPressureTensor - Class in etomica.data.meter
-
Meter for evaluation of the soft-potential pressure tensor in a box.
- MeterPressureTensor(PotentialMaster, Space) - Constructor for class etomica.data.meter.MeterPressureTensor
-
- MeterPressureTensorFromIntegrator - Class in etomica.data.meter
-
Acts as a DataSource to retrieve the pressure from the integrator.
- MeterPressureTensorFromIntegrator(Space) - Constructor for class etomica.data.meter.MeterPressureTensorFromIntegrator
-
- MeterProfile - Class in etomica.data.meter
-
Meter that takes a (scalar) Meter and records its property as a
1-dimensional function of position in the simulation volume.
- MeterProfile(Space, IRandom) - Constructor for class etomica.data.meter.MeterProfile
-
Default constructor sets profile along the x-axis, with 100 points in
the profile.
- MeterProfileByAtoms - Class in etomica.data.meter
-
Meter that takes a (scalar) Meter and records its property as a
1-dimensional function of position in the simulation volume.
- MeterProfileByAtoms(Space) - Constructor for class etomica.data.meter.MeterProfileByAtoms
-
Default constructor sets profile along the y-axis, with 100 histogram points.
- MeterProfileByVolume - Class in etomica.data.meter
-
Meter that takes a (scalar) Meter and records its property as a
1-dimensional function of position in the simulation volume.
- MeterProfileByVolume(Space) - Constructor for class etomica.data.meter.MeterProfileByVolume
-
Default constructor sets profile along the y-axis, with 100 histogram points.
- MeterProfileByVolumeAdsorption - Class in etomica.modules.adsorption
-
- MeterProfileByVolumeAdsorption(Space) - Constructor for class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
-
- MeterPU - Class in etomica.liquidLJ
-
Meter for evaluation of the soft-potential pressure in a box.
- MeterPU(Space) - Constructor for class etomica.liquidLJ.MeterPU
-
- MeterPUCut - Class in etomica.liquidLJ
-
Meter for evaluation of the soft-potential pressure in a box.
- MeterPUCut(Space, double[]) - Constructor for class etomica.liquidLJ.MeterPUCut
-
- MeterPUCutLS - Class in etomica.liquidLJ
-
Meter for evaluation of the soft-potential pressure in a box.
- MeterPUCutLS(Space, int) - Constructor for class etomica.liquidLJ.MeterPUCutLS
-
- MeterRadiusGyration - Class in etomica.data.meter
-
Meter for tabulation of the radius of gyration of a set of chain molecules.
- MeterRadiusGyration(Space) - Constructor for class etomica.data.meter.MeterRadiusGyration
-
- MeterRDF - Class in etomica.data.meter
-
Meter for tabulation of the atomic radial distribution function (RDF).
- MeterRDF(Space) - Constructor for class etomica.data.meter.MeterRDF
-
Creates meter with default to compute pair correlation for all
leaf atoms in a box.
- MeterRDFCylinder - Class in etomica.modules.pistoncylinder
-
MeterRDF sublcass that properly calculates the RDF for the Piston/Cylinder
apparatus.
- MeterRDFCylinder(Space) - Constructor for class etomica.modules.pistoncylinder.MeterRDFCylinder
-
- MeterRDFPC - Class in etomica.data.meter
-
Meter for tabulation of the atomic radial distribution function (RDF).
- MeterRDFPC(Space, PotentialMaster, Box) - Constructor for class etomica.data.meter.MeterRDFPC
-
Creates meter with default to compute pair correlation for all
leaf atoms in a box.
- meterRef - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- meterRefEnergy - Variable in class etomica.normalmode.MeterBoltzmannTarget
-
- MeterRMSD - Class in etomica.data.meter
-
Measured root mean squared displacement of all atoms in the box.
- MeterRMSD(Box, Space) - Constructor for class etomica.data.meter.MeterRMSD
-
- MeterRotationDistributionGroup - Class in etomica.models.nitrogen
-
Meter that measures the spherical coordinate angles
angle[0]: is theta, angle between the projection vector (molecular axis vector onto xy plane)
and x-axis
angle[1]: is phi, angle between the molecular axis vector and z-axis
- MeterRotationDistributionGroup(Box, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.MeterRotationDistributionGroup
-
- MeterRotPerturbMolecule - Class in etomica.models.nitrogen
-
Meter that returns a Boltzmann factor difference between 2 systems: system 1 and 0
1: (Target System) sampled with an angle constraint, e.g.
- MeterRotPerturbMolecule(IntegratorMC, PotentialMaster, ISpecies, Space, Simulation, CoordinateDefinitionNitrogen) - Constructor for class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- meters - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- meters - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- meters - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- meters - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- meters - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- meters - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- meters - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- meters - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- meters - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- meters - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- meters - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- meters - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- meters - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- meters - Variable in class etomica.normalmode.SimOverlap
-
- meters - Variable in class etomica.normalmode.SimOverlapLJ
-
- meters - Variable in class etomica.normalmode.SimOverlapLJModule.APIPotentialReference
-
- meters - Variable in class etomica.normalmode.SimOverlapLJModule
-
- meters - Variable in class etomica.normalmode.SimOverlapModule
-
- meters - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- meters - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- meters - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- meters - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- meters - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- meters - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- meters - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- meters - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- meters - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- meters - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- MeterSamplingHarmonic - Class in etomica.normalmode
-
Meter used for compute for the probability of the harmonic sampling
< e0 / (e1 + alpha * e0)>umb
- MeterSamplingHarmonic(IntegratorBox, MCMoveAtomCoupledUmbrella) - Constructor for class etomica.normalmode.MeterSamplingHarmonic
-
- MeterSamplingTarget - Class in etomica.normalmode
-
Meter used for compute for the probability of the target system sampling
< e1 / (e1 + alpha * e0)>umb
- MeterSamplingTarget(IntegratorBox, MCMoveAtomCoupledUmbrella) - Constructor for class etomica.normalmode.MeterSamplingTarget
-
- MeterSamplingWeight - Class in etomica.virial
-
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
- MeterSamplingWeight(DataSourceAtomDistance) - Constructor for class etomica.virial.MeterSamplingWeight
-
Constructor for MeterVirial.
- MeterSolidDA - Class in etomica.normalmode
-
Meter for evaluation of the soft-potential pressure in a box.
- MeterSolidDA(Space, PotentialMaster, CoordinateDefinition, boolean) - Constructor for class etomica.normalmode.MeterSolidDA
-
- MeterSolidDACut - Class in etomica.normalmode
-
Meter for evaluation of the soft-potential pressure in a box.
- MeterSolidDACut(Space, PotentialMaster, CoordinateDefinition, double[]) - Constructor for class etomica.normalmode.MeterSolidDACut
-
- MeterSolidMirror - Class in etomica.normalmode
-
Meter uses harmonically-mapped averages to compute properties and also
couples configurations with their mirror images to obtain cancellation
of error at very low temperatures.
- MeterSolidMirror(Space, IDataSource, CoordinateDefinition) - Constructor for class etomica.normalmode.MeterSolidMirror
-
- MeterSolidProps - Class in etomica.normalmode
-
- MeterSolidProps(Space, DataSourceScalar, PotentialMaster, CoordinateDefinition, double, double, double, double, double, boolean) - Constructor for class etomica.normalmode.MeterSolidProps
-
- MeterSolidPropsLJ - Class in etomica.normalmode
-
- MeterSolidPropsLJ(Space, DataSourceScalar, PotentialMaster, CoordinateDefinition, double, double, double, double, double, double, double, double, double, double) - Constructor for class etomica.normalmode.MeterSolidPropsLJ
-
- MeterSpin - Class in etomica.spin
-
Meter that provides the x-component of the vector average of
spin values (which is represented by the atom's position
vector).
- MeterSpin(Space) - Constructor for class etomica.spin.MeterSpin
-
- MeterStrain - Class in etomica.modules.materialfracture
-
- MeterStrain() - Constructor for class etomica.modules.materialfracture.MeterStrain
-
- MeterStress - Class in etomica.modules.materialfracture
-
Meter that calculates the stress within the gage cell.
- MeterStress(PotentialCalculationForceStress) - Constructor for class etomica.modules.materialfracture.MeterStress
-
- MeterStructureFactor - Class in etomica.data.meter
-
Meter for calculation of structure factor of atoms for all wave vectors less
than a cutoff.
- MeterStructureFactor(Space, Box, double) - Constructor for class etomica.data.meter.MeterStructureFactor
-
Creates meter with default to compute the structure factor for all atoms
in the box.
- meterTarget - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- meterTarget - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
-
- meterTarget - Variable in class etomica.normalmode.MeterWorkBennetTarget
-
- meterTarget - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- meterTarget - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
-
- MeterTargetRPMolecule - Class in etomica.models.nitrogen
-
Rotational Perturbation for beta-phase Nitrogen
- scaling of the rotational angle to better map the phase space
of the perturbing systems.
- MeterTargetRPMolecule(PotentialMaster, ISpecies, Space, Simulation, CoordinateDefinitionNitrogen, PRotConstraint) - Constructor for class etomica.models.nitrogen.MeterTargetRPMolecule
-
- MeterTargetTP - Class in etomica.normalmode
-
Meter that measures the overlap averages for perturbing from a solid at one
temperature into other the system at other temperatures.
- MeterTargetTP(PotentialMaster, ISpecies, Space, Simulation) - Constructor for class etomica.normalmode.MeterTargetTP
-
- MeterTargetTPMolecule - Class in etomica.models.nitrogen
-
For molecular model, e.g., diatomic Nitrogen model, with 5 d.o.f.
- MeterTargetTPMolecule(PotentialMaster, ISpecies, Space, Simulation) - Constructor for class etomica.models.nitrogen.MeterTargetTPMolecule
-
- meterTemperature - Variable in class etomica.action.BoxQuench
-
- MeterTemperature - Class in etomica.data.meter
-
Meter for measurement of the temperature based on kinetic-energy
equipartition.
- MeterTemperature(Box, int) - Constructor for class etomica.data.meter.MeterTemperature
-
- MeterTemperature(Simulation, Box, int) - Constructor for class etomica.data.meter.MeterTemperature
-
- meterTemperature - Variable in class etomica.integrator.IntegratorGear4NPH
-
- meterTemperature - Variable in class etomica.integrator.IntegratorMD
-
- MeterTensorVelocity - Class in etomica.data.meter
-
A meter to compute the velocity component of the pressure tensor.
- MeterTensorVelocity(Space) - Constructor for class etomica.data.meter.MeterTensorVelocity
-
- MeterThetaDeviation - Class in etomica.normalmode
-
Meter that measures the average tilt angle (not the angle of average tilt!)
- MeterThetaDeviation(Space) - Constructor for class etomica.normalmode.MeterThetaDeviation
-
- MeterTilt - Class in etomica.modules.sam
-
Meter that measures the average tilt angle (not the angle of average tilt!)
- MeterTilt(Space, ISpecies) - Constructor for class etomica.modules.sam.MeterTilt
-
- MeterTilt - Class in etomica.normalmode
-
Meter that measures the average tilt angle (not the angle of average tilt!)
- MeterTilt(Space, ISpecies, int) - Constructor for class etomica.normalmode.MeterTilt
-
- MeterTiltHistogram - Class in etomica.normalmode
-
Meter that measures the average tilt angle (not the angle of average tilt!)
- MeterTiltHistogram(Space, ISpecies) - Constructor for class etomica.normalmode.MeterTiltHistogram
-
- MeterTiltRotation - Class in etomica.normalmode
-
Meter that measures the average tilt angle (not the angle of average tilt!)
- MeterTiltRotation(Space, ISpecies, int) - Constructor for class etomica.normalmode.MeterTiltRotation
-
- MeterTiltRotationHistogram - Class in etomica.normalmode
-
Meter that measures the average tilt angle (not the angle of average tilt!)
- MeterTiltRotationHistogram(Space, ISpecies, int) - Constructor for class etomica.normalmode.MeterTiltRotationHistogram
-
- MeterTiltRotationStdev - Class in etomica.normalmode
-
Meter that measures the average tilt angle (not the angle of average tilt!)
- MeterTiltRotationStdev(Space, ISpecies, int) - Constructor for class etomica.normalmode.MeterTiltRotationStdev
-
- MeterUmbrella - Class in etomica.modules.multiharmonic.umbrella
-
- MeterUmbrella(IDataSource, IDataSource, double) - Constructor for class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
Meter to measure the "overlap" function for free energy calculations,
used as input to an AccumulatorVirialOverlapSingleAverage.
- meterUmbrella - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- MeterVirial - Class in etomica.virial
-
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
- MeterVirial(ClusterAbstract[]) - Constructor for class etomica.virial.MeterVirial
-
Constructor for MeterVirial.
- MeterVirialBD - Class in etomica.virial
-
This meter handles direct sampling with BigDecimal precision for averages.
- MeterVirialBD(ClusterAbstract[]) - Constructor for class etomica.virial.MeterVirialBD
-
Constructor for MeterVirial.
- MeterVirialBDBin - Class in etomica.virial
-
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
- MeterVirialBDBin(ClusterWheatley, IRandom) - Constructor for class etomica.virial.MeterVirialBDBin
-
Constructor for MeterVirial.
- MeterVirialBDBinMultiThreaded - Class in etomica.virial
-
Measures cluster averages for virial coefficients.
- MeterVirialBDBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin) - Constructor for class etomica.virial.MeterVirialBDBinMultiThreaded
-
Constructor for MeterVirial.
- MeterVirialBDBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin, long[], Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, int, boolean) - Constructor for class etomica.virial.MeterVirialBDBinMultiThreaded
-
- MeterVirialBDBinMultiThreaded.MyData - Class in etomica.virial
-
- MeterVirialBinMultiThreaded - Class in etomica.virial
-
Measures cluster averages for virial coefficients.
- MeterVirialBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin) - Constructor for class etomica.virial.MeterVirialBinMultiThreaded
-
Constructor for MeterVirial.
- MeterVirialBinMultiThreaded(ClusterWheatley, IRandom, IntSet.PropertyBin, long[], Map<IntSet, MeterVirialBinMultiThreaded.MyData>, int, boolean) - Constructor for class etomica.virial.MeterVirialBinMultiThreaded
-
- MeterVirialBinMultiThreaded.MyData - Class in etomica.virial
-
- MeterVirialEBinMultiThreaded - Class in etomica.virial
-
Measures cluster averages for virial coefficients.
- MeterVirialEBinMultiThreaded(ClusterWheatleyExtendSW, IRandom, IntSet.PropertyBin, int) - Constructor for class etomica.virial.MeterVirialEBinMultiThreaded
-
Constructor for MeterVirial.
- MeterVirialEBinMultiThreaded(ClusterWheatleyExtendSW, IRandom, IntSet.PropertyBin, long[], Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, int, boolean, int) - Constructor for class etomica.virial.MeterVirialEBinMultiThreaded
-
- MeterVirialEBinMultiThreaded.MyData - Class in etomica.virial
-
- MeterVirialEBinMultiThreaded.MyDataCov - Class in etomica.virial
-
- MeterVirialExternalField - Class in etomica.virial
-
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
- MeterVirialExternalField(ClusterAbstract, double[]) - Constructor for class etomica.virial.MeterVirialExternalField
-
Constructor for MeterVirial.
- MeterVirialExternalFieldConfined - Class in etomica.virial
-
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
- MeterVirialExternalFieldConfined(ClusterAbstract, double[], double[]) - Constructor for class etomica.virial.MeterVirialExternalFieldConfined
-
Constructor for MeterVirial.
- MeterVirialExternalFieldOverlapConfined - Class in etomica.virial
-
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
- MeterVirialExternalFieldOverlapConfined(ExternalVirialDiagrams, MayerFunction, double[], double) - Constructor for class etomica.virial.MeterVirialExternalFieldOverlapConfined
-
Constructor for MeterVirial.
- MeterVirialExternalFieldOverlapConfined.RangeComparator - Class in etomica.virial
-
- MeterVirialExternalFieldOverlapConfinedRho - Class in etomica.virial
-
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
- MeterVirialExternalFieldOverlapConfinedRho(ExternalVirialDiagrams, MayerFunction, double[], double, double, double, double) - Constructor for class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
-
Constructor for MeterVirial.
- MeterVirialExternalFieldOverlapConfinedSW - Class in etomica.virial
-
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
- MeterVirialExternalFieldOverlapConfinedSW(ExternalVirialDiagrams, MayerFunction, double[], double, double, double) - Constructor for class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
-
Constructor for MeterVirial.
- MeterVirialExternalFieldOverlapRho - Class in etomica.virial
-
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
- MeterVirialExternalFieldOverlapRho(ExternalVirialDiagrams, MayerFunction, double[]) - Constructor for class etomica.virial.MeterVirialExternalFieldOverlapRho
-
Constructor for MeterVirial.
- MeterVirialExternalFieldRho - Class in etomica.virial
-
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
- MeterVirialExternalFieldRho(ExternalVirialDiagrams, MayerFunction, double[]) - Constructor for class etomica.virial.MeterVirialExternalFieldRho
-
Constructor for MeterVirial.
- MeterVirialExternalFieldSW - Class in etomica.virial
-
Measures value of clusters in a box and returns the values
divided by the sampling bias from the sampling cluster.
- MeterVirialExternalFieldSW(ClusterAbstract, double[], double, double, double) - Constructor for class etomica.virial.MeterVirialExternalFieldSW
-
Constructor for MeterVirial.
- MeterVirialExternalFieldSW.Near - Class in etomica.virial
-
- MeterVirialIC - Class in etomica.virial
-
Returns cluster and distribution function values from ClusterSumIC
- MeterVirialIC(ClusterSumIC) - Constructor for class etomica.virial.MeterVirialIC
-
Constructor for MeterVirial.
- MeterVirialSWWE - Class in etomica.virial
-
- MeterVirialSWWE(ClusterWheatleyExtendSW) - Constructor for class etomica.virial.MeterVirialSWWE
-
- MeterViscosity - Class in etomica.modules.rheology
-
Meter to measure the viscosity of a polymer in a shear field.
- MeterViscosity(Space) - Constructor for class etomica.modules.rheology.MeterViscosity
-
- MeterVolume - Class in etomica.data.meter
-
Meter for measurement of the box volume.
- MeterVolume() - Constructor for class etomica.data.meter.MeterVolume
-
- MeterWallForce - Class in etomica.interfacial
-
- MeterWallForce(Space, PotentialMaster, Box, ISpecies) - Constructor for class etomica.interfacial.MeterWallForce
-
- MeterWallForce.PotentialCalculationWallForce - Class in etomica.interfacial
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- MeterWallPosition - Class in etomica.interfacial
-
- MeterWallPosition(Box, ISpecies, double) - Constructor for class etomica.interfacial.MeterWallPosition
-
- MeterWallPressure - Class in etomica.modules.sam
-
- MeterWallPressure(PotentialCalculationForceSumWall) - Constructor for class etomica.modules.sam.MeterWallPressure
-
- meterWidom - Variable in class etomica.modules.insertion.InsertionGraphic
-
- MeterWidom() - Constructor for class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- MeterWidomInsertion - Class in etomica.data.meter
-
Meter to measure the chemical potential (as its exponent: exp(-mu/kT)) of a
species via the Widom insertion method.
- MeterWidomInsertion(Space, IRandom) - Constructor for class etomica.data.meter.MeterWidomInsertion
-
- MeterWidomInsertionCorrection - Class in etomica.liquidLJ
-
Meter to measure the chemical potential (as its exponent: exp(-mu/kT)) of a
species via the Widom insertion method.
- MeterWidomInsertionCorrection(Space, IRandom) - Constructor for class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- MeterWidomInsertionP - Class in etomica.liquidLJ
-
Meter to measure the chemical potential (as its exponent: exp(-mu/kT)) of a
species via the Widom insertion method.
- MeterWidomInsertionP(Space, IRandom) - Constructor for class etomica.liquidLJ.MeterWidomInsertionP
-
- MeterWidomMode - Class in etomica.models.oneDHardRods
-
Uses a Widom-like insertion of a mode to calculate a probability.
- MeterWidomMode(String, PotentialMaster, CoordinateDefinition, Box, int) - Constructor for class etomica.models.oneDHardRods.MeterWidomMode
-
- MeterWidomModeImaginary - Class in etomica.models.oneDHardRods
-
Uses a Widom-like insertion of a mode to calculate a probability.
- MeterWidomModeImaginary(String, PotentialMaster, CoordinateDefinition, Box, int) - Constructor for class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- MeterWidomModeReal - Class in etomica.models.oneDHardRods
-
Uses a Widom-like insertion of a mode to calculate a probability.
- MeterWidomModeReal(String, PotentialMaster, CoordinateDefinition, Box, int) - Constructor for class etomica.models.oneDHardRods.MeterWidomModeReal
-
- MeterWorkABandReweighting - Class in etomica.gaussianwork
-
Meter used for multiharmonic overlap sampling in the A-sampled system.
- MeterWorkABandReweighting(IntegratorBox, PotentialMaster, double) - Constructor for class etomica.gaussianwork.MeterWorkABandReweighting
-
- MeterWorkBAandReweighting - Class in etomica.gaussianwork
-
Meter used for overlap sampling in the B-sampled system.
- MeterWorkBAandReweighting(IntegratorBox, PotentialMaster, double) - Constructor for class etomica.gaussianwork.MeterWorkBAandReweighting
-
- MeterWorkBennetHarmonic - Class in etomica.normalmode
-
Meter used for direct sampling in the harmonic-sampled system.
- MeterWorkBennetHarmonic(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterWorkBennetHarmonic
-
- MeterWorkBennetTarget - Class in etomica.normalmode
-
Meter used for direct sampling in the target-sampled system.
- MeterWorkBennetTarget(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterWorkBennetTarget
-
- MeterWorkHarmonicBennet - Class in etomica.normalmode
-
Meter used for overlap sampling in the harmonic-sampled system.
- MeterWorkHarmonicBennet(MCMoveHarmonic, PotentialMaster, double) - Constructor for class etomica.normalmode.MeterWorkHarmonicBennet
-
- MeterWorkHarmonicPhaseSpace - Class in etomica.normalmode
-
Meter used for overlap sampling in the harmonic-sampled system.
- MeterWorkHarmonicPhaseSpace(MCMoveHarmonic, PotentialMaster) - Constructor for class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- MeterWorkHarmonicTargetandReweighting - Class in etomica.normalmode
-
Meter used for overlap sampling in the harmonic-sampled system.
- MeterWorkHarmonicTargetandReweighting(MCMoveHarmonic, PotentialMaster, double) - Constructor for class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- MeterWorkHarmonicUmbrella - Class in etomica.normalmode
-
Meter used for direct sampling in the harmonic-sampled system.
- MeterWorkHarmonicUmbrella(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- MeterWorkTargetBennet - Class in etomica.normalmode
-
Meter used for overlap sampling in the target-sampled system.
- MeterWorkTargetBennet(IntegratorBox, MeterHarmonicEnergy, double) - Constructor for class etomica.normalmode.MeterWorkTargetBennet
-
- MeterWorkTargetHarmonicandReweighting - Class in etomica.normalmode
-
Meter used for overlap sampling in the target-sampled system.
- MeterWorkTargetHarmonicandReweighting(IntegratorBox, MeterHarmonicEnergy, double) - Constructor for class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- MeterWorkTargetPhaseSpace - Class in etomica.normalmode
-
Meter used for overlap sampling in the target-sampled system.
- MeterWorkTargetPhaseSpace(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- MeterWorkTargetUmbrella - Class in etomica.normalmode
-
Meter used for direct sampling in the target-sampled system.
- MeterWorkTargetUmbrella(IntegratorBox, MeterHarmonicEnergy) - Constructor for class etomica.normalmode.MeterWorkTargetUmbrella
-
- MeterWorkUmbrellaHarmonic - Class in etomica.normalmode
-
Meter used for direct sampling in the harmonic-sampled system.
- MeterWorkUmbrellaHarmonic(IntegratorBox, MCMoveAtomCoupledUmbrella) - Constructor for class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- MeterWorkUmbrellaTarget - Class in etomica.normalmode
-
Meter used for direct sampling in the target-sampled system.
- MeterWorkUmbrellaTarget(IntegratorBox, MCMoveAtomCoupledUmbrella) - Constructor for class etomica.normalmode.MeterWorkUmbrellaTarget
-
- MethanolPotentialHelper - Class in etomica.models.rowley
-
- MethanolPotentialHelper() - Constructor for class etomica.models.rowley.MethanolPotentialHelper
-
- MethanolPotentialHelper - Class in etomica.models.traPPE
-
- MethanolPotentialHelper() - Constructor for class etomica.models.traPPE.MethanolPotentialHelper
-
- MethanolRouteParams - Class in etomica.models.rowley
-
- MethanolRouteParams() - Constructor for class etomica.models.rowley.MethanolRouteParams
-
- MethodNotImplementedException - Exception in etomica.exception
-
Exception that indicates a method is defined for a class (perhaps to adhere
to an interface), but its implementation is not yet completed.
- MethodNotImplementedException() - Constructor for exception etomica.exception.MethodNotImplementedException
-
Constructor for MethodNotImplementedException.
- MethodNotImplementedException(String) - Constructor for exception etomica.exception.MethodNotImplementedException
-
Constructor for MethodNotImplementedException.
- MethodNotImplementedException(String, Throwable) - Constructor for exception etomica.exception.MethodNotImplementedException
-
Constructor for MethodNotImplementedException.
- MethodNotImplementedException(Throwable) - Constructor for exception etomica.exception.MethodNotImplementedException
-
Constructor for MethodNotImplementedException.
- metricPanel - Variable in class etomica.graphics.SimulationPanel
-
- MEv1v2(Vector, Vector) - Method in interface etomica.space.Tensor
-
"Minus equals" (-=) operation with a dyad argument.
- MEv1v2(Vector, Vector) - Method in class etomica.space1d.Tensor1D
-
- MEv1v2(Vector, Vector) - Method in class etomica.space2d.Tensor2D
-
- MEv1v2(Vector, Vector) - Method in class etomica.space3d.Tensor3D
-
- MEv1v2(Vector, Vector) - Method in class etomica.spaceNd.TensorND
-
- mfp - Variable in class etomica.graph.operations.ComponentSubst.ComponentSubstParameters
-
- mfp - Variable in class etomica.graph.operations.Decorate.DecorateParameters
-
- mfp - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
-
- mfp - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
-
- mfp - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- mfp - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- mfp - Variable in class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
-
- mH - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- mH2O - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- millerPlane - Variable in class etomica.dimer.SimDimerMEAMGB
-
- millerRabin(BigInteger) - Method in class etomica.veos.bigdecimal.Prime
-
Miller-Rabin primality tests.
- mimeTypeMap - Static variable in class etomica.graph.view.rasterizer.Main
-
Static map containing all the mime types understood by the
rasterizer
- min(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor
-
Minimum of two values.
- min(Vector<Ifactor>) - Static method in class etomica.veos.bigdecimal.Ifactor
-
Minimum of a list of values.
- min(Rational) - Method in class etomica.veos.bigdecimal.Rational
-
Compares the value of this with another constant.
- min - Static variable in class org.jmol.script.Token
-
- MIN_INT - Static variable in class etomica.veos.bigdecimal.Rational
-
- MIN_X - Static variable in class etomica.graphics.DevicePlotPoints
-
- MIN_Y - Static variable in class etomica.graphics.DevicePlotPoints
-
- minAdjustStep - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
-
- minbonddistance - Static variable in class org.jmol.script.Token
-
- mincf - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
-
- minDiffLocation() - Method in class etomica.virial.overlap.DataSourceVirialOverlap
-
Returns the index of the Bennet parameter which minimizes the differences
between the Bennet "sums" from the target and references accumulators.
- minDiffLocation() - Method in class etomica.virial.overlap.DataVirialOverlap
-
Deprecated.
- minDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- minFlipDistance - Variable in class etomica.virial.ClusterCoupledFlipped
-
- minFlipDistance - Variable in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- minFloat - Variable in class etomica.graphics.DisplayTable
-
- minFound - Variable in class etomica.dimer.IntegratorDimerMin
-
- MINIMIZATION_ATOM_MAX - Static variable in class org.jmol.viewer.JmolConstants
-
- MinimizationBetaNitrogenModel - Class in etomica.models.nitrogen
-
Lattice-Energy Minimization for Beta-Nitrogen Structure
using gradient
- MinimizationBetaNitrogenModel(Space, int[], double) - Constructor for class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- MinimizationBetaNitrogenModelLS - Class in etomica.models.nitrogen
-
Lattice-Energy Minimization for Beta-Nitrogen Structure
using gradient with lattice sum
- MinimizationBetaNitrogenModelLS(Space, double, double) - Constructor for class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- minimizationcriterion - Static variable in class org.jmol.script.Token
-
- minimizationrefresh - Static variable in class org.jmol.script.Token
-
- minimizationsilent - Static variable in class org.jmol.script.Token
-
- minimizationsteps - Static variable in class org.jmol.script.Token
-
- MinimizationTIP4P - Class in etomica.models.clathrates
-
- MinimizationTIP4P(Space, double, double, double[], int[], int, boolean, double, String, boolean) - Constructor for class etomica.models.clathrates.MinimizationTIP4P
-
- MinimizationTIP4P.ChargeAgentSourceRPM - Class in etomica.models.clathrates
-
- MinimizationTIP4P.SimParams - Class in etomica.models.clathrates
-
- minimize(double[], double, int) - Method in class etomica.math.numerical.NewtonMinimization
-
- minimize(double[], double[], double, int) - Method in class etomica.math.numerical.SteepestDescent
-
- MINIMIZE_FIXED_RANGE - Static variable in class org.jmol.viewer.JmolConstants
-
- MinimizeBetaNitrogenLatticeParameter - Class in etomica.models.nitrogen
-
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are:
unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
- 3 translational + 2 rotational
There are total of 20 degrees of freedom.
- MinimizeBetaNitrogenLatticeParameter(Space, int[], double) - Constructor for class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- MinimizeBetaNitrogenLatticeParameterFromFile - Class in etomica.models.nitrogen
-
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are:
unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
- 3 translational + 2 rotational
There are total of 20 degrees of freedom.
- MinimizeBetaNitrogenLatticeParameterFromFile(Space, int[], double, double[]) - Constructor for class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- MinimizeBetaNitrogenLatticeParameterLSFromFile - Class in etomica.models.nitrogen
-
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are:
unit cell A: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
unit cell B: molecule 1 (u[0] through u[4]) and molecule 2 (u[5] through u[9])
- 3 translational + 2 rotational
There are total of 20 degrees of freedom.
- MinimizeBetaNitrogenLatticeParameterLSFromFile(Space, double, double[], double) - Constructor for class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- MinimizeBetaNitrogenTranslationDOF - Class in etomica.models.nitrogen
-
This class is written to minimize the lattice energy of the beta-phase
Nitrogen, which has HCP packing with 2 basis atoms using line minimization
The varying parameters are all the translational d.o.f of the molecules
NO rotational d.o.f.
- MinimizeBetaNitrogenTranslationDOF(Space, int[], double, String, double) - Constructor for class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- MinimizeGammaNitrogenLatticeParameter - Class in etomica.models.nitrogen
-
Determine c/a ratio for tetragonal unit cell that minimizes
the lattice energy of gamma-N2 crystal structure
gamma-N2 crystal Structure
- MinimizeGammaNitrogenLatticeParameter(Space, int, double, double) - Constructor for class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- MinimizeHCP - Class in etomica.normalmode
-
Determines c/a ratio of primitive vector lengths corresponding to the
minimum energy HCP structure.
- MinimizeHCP(Space, int, double, int, double, double) - Constructor for class etomica.normalmode.MinimizeHCP
-
- MinimizeHCP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- minimum() - Method in class etomica.math.DoubleRange
-
The minimium defined by this range.
- minimum(P2QChemInterpolated) - Method in class etomica.potential.P2QChemInterpolated
-
- minimumScreening(int, int, double, double) - Method in class etomica.math.numerical.VirialOptimizer
-
- minMulti - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- minMulti - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- minMultiP - Variable in class etomica.virial.cluster.VirialDiagrams
-
- minMultiP - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- minN - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- minNumAtoms - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- minOCOr2 - Variable in class etomica.modules.catalysis.P2SquareWellBonding
-
- minOOr2 - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- minor(BigInteger[][], int, int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Minor of an integer matrix.
- minpixelselradius - Static variable in class org.jmol.script.Token
-
- minR - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- minR2 - Variable in class etomica.association.AssociationHelperBranched
-
- minR2 - Variable in class etomica.association.AssociationHelperDouble
-
- minR2 - Variable in class etomica.association.AssociationHelperMolecule
-
- minRadicalSites - Variable in class etomica.modules.catalysis.P2SquareWellSurface
-
- minSearch - Variable in class etomica.dimer.SimDimerLJadatom
-
- minus(Complex) - Method in class etomica.math.Complex
-
Subtraction of Complex numbers (doesn't change this Complex number).
- minus_half_sqrt_bondlength - Static variable in class etomica.virial.ConformationPh3site
-
- mip - Variable in class etomica.graph.property.FFTDecomposition
-
- mip - Variable in class etomica.graph.property.IsFFT
-
- MIXED - Static variable in class etomica.units.dimensions.Dimension
-
Dimension used to indicate that a group of values are not all of
the same dimension.
- mixF - Variable in class etomica.virial.ClusterWheatleySoftBDMix
-
- mixF - Variable in class etomica.virial.ClusterWheatleySoftMix
-
- mixFMulti3 - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
-
- mixID - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
-
- mixPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
-
- mixPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
-
- mixPotentialsM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- mixPotentialsP - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- MKS - Class in etomica.units.systems
-
Meter-Kilogram-Second system of units
- MKS() - Constructor for class etomica.units.systems.MKS
-
- mLREP - Variable in class etomica.meam.PotentialCuLREP
-
- mmBond - Variable in class etomica.virial.cluster.VirialDiagrams
-
- mmBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- mNumBody - Variable in class etomica.virial.cluster.ClusterDiagram
-
- mNumIdenticalPermutations - Variable in class etomica.virial.cluster.ClusterDiagram
-
- mO - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- mo - Static variable in class org.jmol.script.Token
-
- mobileSpecies - Variable in class etomica.config.GrainBoundaryTiltConfiguration
-
- mod() - Method in class etomica.space.BenchVector3D
-
- mod(Vector) - Method in interface etomica.space.Vector
-
Replaces each component of this vector with its value modulo
the corresponding component in u
- mod(Vector) - Method in class etomica.space1d.Vector1D
-
- mod(Vector1D) - Method in class etomica.space1d.Vector1D
-
- mod(Vector) - Method in class etomica.space2d.Vector2D
-
- mod(Vector) - Method in class etomica.space3d.Vector3D
-
- mod(Vector3D) - Method in class etomica.space3d.Vector3D
-
- mod(Vector) - Method in class etomica.spaceNd.VectorND
-
- mod2pi(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Reduce value to the interval [0,2*Pi].
- Model - Class in etomica.chem.models
-
Top-level class for a molecular model.
- Model(boolean) - Constructor for class etomica.chem.models.Model
-
- model - Static variable in class org.jmol.script.Token
-
- Model.PotentialAndIterator - Class in etomica.chem.models
-
Wrapper class for a Potential and an AtomsetIteratorBasisDependent that
is associated with the potential.
- ModelAlertMsgDialog - Class in etomica.virial.GUI.models
-
- ModelAlertMsgDialog(String) - Constructor for class etomica.virial.GUI.models.ModelAlertMsgDialog
-
- ModelAlkaneLengthSelection - Class in etomica.virial.GUI.models
-
- ModelAlkaneLengthSelection() - Constructor for class etomica.virial.GUI.models.ModelAlkaneLengthSelection
-
- ModelChain - Class in etomica.chem.models
-
Model class for a simple chain molecule (homopolymer)
- ModelChain(Space, boolean) - Constructor for class etomica.chem.models.ModelChain
-
Constructs a default ModelChain instance.
- modelindex - Static variable in class org.jmol.script.Token
-
- modelIndex - Variable in class org.jmol.util.Point3fi
-
- MODELKIT_ZAP_STRING - Static variable in class org.jmol.viewer.JmolConstants
-
- MODELKIT_ZAP_TITLE - Static variable in class org.jmol.viewer.JmolConstants
-
- modelkitmode - Static variable in class org.jmol.script.Token
-
- ModelMoleculeListDisplayTable - Class in etomica.virial.GUI.models
-
- ModelMoleculeListDisplayTable() - Constructor for class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- ModelMoleculeListDisplayTable_new - Class in etomica.virial.GUI.models
-
- ModelMoleculeListDisplayTable_new() - Constructor for class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- ModelPotParamDisplayTable - Class in etomica.virial.GUI.models
-
- ModelPotParamDisplayTable() - Constructor for class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- modelSelectedSpecies - Variable in class etomica.virial.GUI.models.AppModelMixtureBuilder
-
- ModelSelectedSpecies - Class in etomica.virial.GUI.models
-
- ModelSelectedSpecies() - Constructor for class etomica.virial.GUI.models.ModelSelectedSpecies
-
- ModelSimulationConstructor - Class in etomica.virial.GUI.models
-
- ModelSimulationConstructor() - Constructor for class etomica.virial.GUI.models.ModelSimulationConstructor
-
- ModelSimulationEnvironment - Class in etomica.virial.GUI.models
-
- ModelSimulationEnvironment() - Constructor for class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- ModelSimulationEnvironment(double, int, ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- ModelSimulationEnvironment(double, int) - Constructor for class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- modelSpeciesSelection - Variable in class etomica.virial.GUI.models.AppModelMixtureBuilder
-
- ModelSpeciesSelection - Class in etomica.virial.GUI.models
-
- ModelSpeciesSelection() - Constructor for class etomica.virial.GUI.models.ModelSpeciesSelection
-
- ModelTemperatureAndSteps - Class in etomica.virial.GUI.models
-
- modeNum - Variable in class etomica.normalmode.MCMoveHarmonic
-
- modes - Variable in class etomica.normalmode.MCMoveHarmonicStep
-
- modeSigns - Variable in class etomica.dimer.SimDimerLJadatom
-
- modeSigns - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- modeSigns - Variable in class etomica.dimer.SimDimerMEAMGB
-
- modeSigns - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- Modifier - Interface in etomica.modifier
-
A Modifier object permits changes to be made to a property of another object.
- ModifierAtomDiameter(MuGraphic, SpeciesSpheresMono, P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide) - Constructor for class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- ModifierAtomDiameter() - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
-
- ModifierAtomDiameter(SpeciesSpheresMono, P2LennardJones, SpeciesSpheresMono[], P2LennardJones[], DiameterHashByType) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- ModifierAtomDiameter(SpeciesSpheresMono, P2LennardJones, P2LennardJones[], P2LennardJones[], DiameterHashByType) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- ModifierAtomDiameter() - Constructor for class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
-
- ModifierBoolean - Interface in etomica.modifier
-
Interface that permits changes to be made to a boolean property of another object.
- ModifierBoxSize(Space, Box, int, IAction) - Constructor for class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- ModifierBoxSize(Space, Box, int, IAction) - Constructor for class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- ModifierCells3D - Class in etomica.normalmode
-
Modifier class that enables change of the number of cells in 2D
- ModifierCells3D(Box, ISpecies) - Constructor for class etomica.normalmode.ModifierCells3D
-
- ModifierConfiguration(Box, List<Vector[]>, List<Vector[]>, List<DataFunction>, List<DataFunction.DataInfoFunction>, DataTag) - Constructor for class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- ModifierDimensions - Class in etomica.modules.entropylottery
-
- ModifierDimensions(Space, Box) - Constructor for class etomica.modules.entropylottery.ModifierDimensions
-
- ModifierEpsilon(P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide, IntegratorBox) - Constructor for class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- ModifierEpsilon(P2LennardJones, P2LennardJones[], P2LennardJones[]) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
-
- ModifierEpsilon(P2LennardJones, P2LennardJones[], P2LennardJones[]) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
-
- ModifierFunctionWrapper - Class in etomica.modifier
-
Extends the configurable modifier to permit a function to be applied to
a value before the modified property is set.
- ModifierFunctionWrapper(Object[], String) - Constructor for class etomica.modifier.ModifierFunctionWrapper
-
- ModifierFunctionWrapper(Object, String) - Constructor for class etomica.modifier.ModifierFunctionWrapper
-
- ModifierGeneral - Class in etomica.modifier
-
Implements the Modifier functionality using introspection to obtain the accessor methods for a property.
- ModifierGeneral(Object[], String) - Constructor for class etomica.modifier.ModifierGeneral
-
Constructor connecting the modifier's getValue and setValue methods to the set/get accessor
methods of the object being modifier.
- ModifierGeneral(Object, String) - Constructor for class etomica.modifier.ModifierGeneral
-
Modifier for property of a single object (most common use)
- ModifierLambda(P2SquareWellOneSide, P2SquareWellOneSide, P2SquareWellOneSide, IntegratorBox) - Constructor for class etomica.modules.mu.MuGraphic.ModifierLambda
-
- ModifierNMolecule - Class in etomica.modifier
-
Modifier class that enables change of the number of molecules of a particular species
in a particular box.
- ModifierNMolecule(Box, ISpecies) - Constructor for class etomica.modifier.ModifierNMolecule
-
- ModifierPistonDensity() - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
-
- ModifierPistonPressure - Class in etomica.modules.pistoncylinder
-
Modifier for the piston pressure.
- ModifierPistonPressure(Space, P1HardMovingBoundary, Dimension) - Constructor for class etomica.modules.pistoncylinder.ModifierPistonPressure
-
- ModifierPMu - Class in etomica.modules.adsorption
-
- ModifierPMu(P2SquareWell, IntegratorBox, EOSSW, MyMCMove, MeterExcessAdsorbed) - Constructor for class etomica.modules.adsorption.ModifierPMu
-
- ModifierSoluteCharge(P2Electrostatic, P2Electrostatic, P2Electrostatic, P2Electrostatic[], P2Electrostatic[]) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- ModifierTPI - Class in etomica.virial.simulations
-
- ModifierTPI(double, int, MCMoveClusterRingRegrow, MCMoveClusterRingRegrow, ClusterAbstract) - Constructor for class etomica.virial.simulations.ModifierTPI
-
- ModifierWallPosition(Sam) - Constructor for class etomica.modules.sam.SamGraphic.ModifierWallPosition
-
- ModifierXCells2D - Class in etomica.normalmode
-
Modifier class that enables change of the number of cells in 2D
- ModifierXCells2D(Box, ISpecies, int) - Constructor for class etomica.normalmode.ModifierXCells2D
-
- ModifierYCells2D - Class in etomica.normalmode
-
Modifier class that enables change of the number of cells in 2D
- ModifierYCells2D(Box, ISpecies, int) - Constructor for class etomica.normalmode.ModifierYCells2D
-
- modify - Static variable in class org.jmol.script.Token
-
- modifyAction - Variable in class etomica.graphics.DeviceBox
-
Modifier connecting the slider to the property
- modifyAction - Variable in class etomica.graphics.DeviceCheckBox
-
- modifyAction - Variable in class etomica.graphics.DeviceSlider
-
Modifier connecting the slider to the property
- modifyAction - Variable in class etomica.graphics.DeviceSpinner
-
Modifier connecting the spinner to the property
- ModifyAction - Class in etomica.modifier
-
Wraps a Modifier instance so that the modification can be performed
as the consequence of an action.
- ModifyAction(Modifier) - Constructor for class etomica.modifier.ModifyAction
-
Constuctor requires the wrapped Modifier, which is final.
- ModifyBooleanAction - Class in etomica.modifier
-
Wraps a ModifierBoolean instance so that the modification can be performed
as the consequence of an action.
- ModifyBooleanAction(ModifierBoolean) - Constructor for class etomica.modifier.ModifyBooleanAction
-
Constuctor requires the wrapped ModifierBoolean
- modifyorcreate - Static variable in class org.jmol.script.Token
-
- modpi(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Reduce value to the interval [-Pi/2,Pi/2].
- moduleNum - Variable in class etomica.modules.statistics.StatisticsMCGraphic.StatsParams
-
- modulus() - Method in class etomica.math.Complex
-
Modulus of this Complex number, the distance from the origin in polar coordinates.
- moebius() - Method in class etomica.veos.bigdecimal.Ifactor
-
The Moebius function.
- molAVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- molAVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- molAxis - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- molBVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- molBVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- Mole - Class in etomica.units
-
The mole unit of quantity, approximately equal to 6.022e23 simulation units.
- molecOrientation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- molecOrientation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- MolecularModel2CLJQ_SpeciesCO2 - Class in etomica.virial.GUI.models
-
- MolecularModel2CLJQ_SpeciesCO2() - Constructor for class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- MolecularModel2CLJQ_SpeciesEthane - Class in etomica.virial.GUI.models
-
- MolecularModel2CLJQ_SpeciesEthane() - Constructor for class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- MolecularModel2CLJQ_SpeciesLJ - Class in etomica.virial.GUI.models
-
- MolecularModel2CLJQ_SpeciesLJ() - Constructor for class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- MolecularModelEMP2_SpeciesCO2 - Class in etomica.virial.GUI.models
-
- MolecularModelEMP2_SpeciesCO2() - Constructor for class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- MolecularModelExp6_SpeciesAlkane - Class in etomica.virial.GUI.models
-
- MolecularModelExp6_SpeciesAlkane() - Constructor for class etomica.virial.GUI.models.MolecularModelExp6_SpeciesAlkane
-
- MolecularModelLJ_SpeciesLJ - Class in etomica.virial.GUI.models
-
- MolecularModelLJ_SpeciesLJ() - Constructor for class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- MolecularModelLJQ_SpeciesLJ - Class in etomica.virial.GUI.models
-
- MolecularModelLJQ_SpeciesLJ() - Constructor for class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- MolecularModelSKS_SpeciesAlkane - Class in etomica.virial.GUI.models
-
- MolecularModelSKS_SpeciesAlkane() - Constructor for class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- MolecularModelSKS_SpeciesAlkane(int) - Constructor for class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- MolecularModelSPCE_SpeciesH2O - Class in etomica.virial.GUI.models
-
- MolecularModelSPCE_SpeciesH2O() - Constructor for class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- MolecularModelTRAPPE_SpeciesAlkane - Class in etomica.virial.GUI.models
-
- MolecularModelTRAPPE_SpeciesAlkane() - Constructor for class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- MolecularModelTRAPPE_SpeciesAlkane(int) - Constructor for class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- MolecularModelTrappe_SpeciesCO2 - Class in etomica.virial.GUI.models
-
- MolecularModelTrappe_SpeciesCO2() - Constructor for class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- molecularPotentials - Variable in class etomica.potential.PotentialMasterLrc
-
- MolecularWeightAvg - Class in etomica.modules.chainequilibrium
-
Takes output from MeterChainLength as input and outputs the number-average
molecular weight.
- MolecularWeightAvg() - Constructor for class etomica.modules.chainequilibrium.MolecularWeightAvg
-
- MolecularWeightAvg2 - Class in etomica.modules.chainequilibrium
-
Takes output from MeterChainLength as input and outputs the weight-average
molecular weight.
- MolecularWeightAvg2() - Constructor for class etomica.modules.chainequilibrium.MolecularWeightAvg2
-
- molecule - Variable in class etomica.box.BoxMoleculeEvent
-
- molecule - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- molecule - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- Molecule - Class in etomica.molecule
-
- Molecule(ISpecies, int) - Constructor for class etomica.molecule.Molecule
-
- molecule - Static variable in class org.jmol.script.Token
-
- molecule0 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- molecule0 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- molecule0 - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- molecule0 - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- molecule1 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- molecule1 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- molecule1 - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- molecule1 - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- MOLECULE1_INDEX - Static variable in class etomica.util.Debug
-
Molecule index of a molecule of interest.
- MOLECULE2_INDEX - Static variable in class etomica.util.Debug
-
Global index of a molecule of interest.
- MoleculeAction - Interface in etomica.action
-
Interface for a class that can perform an action on an atom.
- MoleculeActionRelaxWater3P - Class in etomica.virial
-
- MoleculeActionRelaxWater3P(Space) - Constructor for class etomica.virial.MoleculeActionRelaxWater3P
-
- MoleculeActionTranslateTo - Class in etomica.action
-
Moves (translates) an atom to a specified position.
- MoleculeActionTranslateTo(Space) - Constructor for class etomica.action.MoleculeActionTranslateTo
-
Creates new action with atom position defined by its
center of mass (via MoleculePositionCOM).
- moleculeAdded(IMolecule) - Method in class etomica.box.BoxEventManager
-
- MoleculeAgent(Space) - Constructor for class etomica.integrator.IntegratorRigidIterative.MoleculeAgent
-
- MoleculeAgent(Space) - Constructor for class etomica.integrator.IntegratorRigidMatrixIterative.MoleculeAgent
-
- MoleculeAgent(Space) - Constructor for class etomica.rotation.IntegratorVelocityVerletQuaternion.MoleculeAgent
-
- moleculeAgentManager - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- moleculeAgentManager - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- moleculeAgentManager - Variable in class etomica.integrator.IntegratorRigidIterative
-
- moleculeAgentManager - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- MoleculeAgentManager<E> - Class in etomica.molecule
-
MoleculeAgentManager acts on behalf of client classes (an AgentSource) to
manage agents in every IMolecule in a box.
- MoleculeAgentManager(Simulation, Box, MoleculeAgentManager.MoleculeAgentSource<E>) - Constructor for class etomica.molecule.MoleculeAgentManager
-
- MoleculeAgentManager(Simulation, Box, Function<IMolecule, ? extends E>) - Constructor for class etomica.molecule.MoleculeAgentManager
-
- MoleculeAgentManager(Simulation, Box, Function<IMolecule, ? extends E>, BiConsumer<? super E, IMolecule>) - Constructor for class etomica.molecule.MoleculeAgentManager
-
- moleculeAgentManager - Variable in class etomica.potential.PotentialCalculationTorqueSum
-
- moleculeAgentManager - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- MoleculeAgentManager.MoleculeAgentSource<E> - Interface in etomica.molecule
-
Interface for an object that wants an agent associated with each
IMolecule a Box.
- MoleculeArrayList - Class in etomica.molecule
-
- MoleculeArrayList() - Constructor for class etomica.molecule.MoleculeArrayList
-
- MoleculeArrayList(int) - Constructor for class etomica.molecule.MoleculeArrayList
-
- moleculeCell0 - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- moleculeCenter - Variable in class etomica.action.BoxInflate
-
- moleculeCenter - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- moleculeCenter - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- MoleculeChildAtomAction - Class in etomica.action
-
Wraps an AtomAction, and performs the wrapped action on the atom
only if it is a leaf atom; if given an atom group (as indicated
by the atom's node), performs action instead on all the atom's
child atoms.
- MoleculeChildAtomAction(AtomAction) - Constructor for class etomica.action.MoleculeChildAtomAction
-
Constructor takes wrapped action, which is final.
- moleculeForce - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
-
- moleculeIndexChanged(IMolecule, int) - Method in class etomica.box.BoxEventManager
-
- moleculeIndices - Variable in class etomica.virial.ClusterWheatleyMultibody
-
- moleculeIndices - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
-
- moleculeIndices - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- moleculeIndices - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- moleculeIndices - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
-
- MoleculeInfoBrute(Space) - Constructor for class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- moleculeIterator - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- MoleculeIterator - Interface in etomica.molecule.iterator
-
Interface for classes that loop over a set of atoms.
- MoleculeIterator0() - Constructor for class etomica.potential.PotentialMaster.MoleculeIterator0
-
- MoleculeIteratorAll - Class in etomica.molecule.iterator
-
Iterator for all the molecules of a set of species in a box.
- MoleculeIteratorAll(ISpecies[]) - Constructor for class etomica.molecule.iterator.MoleculeIteratorAll
-
- MoleculeIteratorAll(ISpecies[], boolean) - Constructor for class etomica.molecule.iterator.MoleculeIteratorAll
-
- MoleculeIteratorAllMolecules - Class in etomica.molecule.iterator
-
Iterator for all the molecules in a box.
- MoleculeIteratorAllMolecules() - Constructor for class etomica.molecule.iterator.MoleculeIteratorAllMolecules
-
- MoleculeIteratorAllMolecules(Box) - Constructor for class etomica.molecule.iterator.MoleculeIteratorAllMolecules
-
Returns a new iterator ready to iterate over the molecules of the given
box.
- MoleculeIteratorArrayList - Class in etomica.molecule.iterator
-
An atom iterator of the elements from an AtomArrayList (in proper
sequence).
- MoleculeIteratorArrayList(IteratorDirective.Direction, int, MoleculeToIndex, MoleculeToMoleculeList) - Constructor for class etomica.molecule.iterator.MoleculeIteratorArrayList
-
- MoleculeIteratorArrayListSimple - Class in etomica.molecule.iterator
-
An atom iterator of the elements from an AtomArrayList (in proper
sequence).
- MoleculeIteratorArrayListSimple() - Constructor for class etomica.molecule.iterator.MoleculeIteratorArrayListSimple
-
Constructs new iterator with an empty list.
- MoleculeIteratorArrayListSimple(IMoleculeList) - Constructor for class etomica.molecule.iterator.MoleculeIteratorArrayListSimple
-
Constructs new iterator set to iterate given list (upon reset).
- MoleculeIteratorBoxDependent - Interface in etomica.molecule.iterator
-
Interface indicating that an atom iterator can determine appropriate
atoms for iteration given an arbitrary box.
- MoleculeIteratorCell - Class in etomica.nbr.cell.molecule
-
Returns occupants of all cells as iterates.
- MoleculeIteratorCell(int, BoxAgentManager) - Constructor for class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
Constructor makes iterator that must have box specified and then be
reset() before iteration.
- MoleculeIteratorMolecule - Class in etomica.molecule.iterator
-
Iterator for the molecules of a single species in a box.
- MoleculeIteratorMolecule(ISpecies) - Constructor for class etomica.molecule.iterator.MoleculeIteratorMolecule
-
- MoleculeIteratorMoleculeDependent - Interface in etomica.molecule.iterator
-
Interface for an atom iterator that can be altered by setting
of an atom.
- MoleculeIteratorSinglet - Class in etomica.molecule.iterator
-
Iterator that expires after returning a single atom, which is
specified by a call to the setAtom method, or via the constructor.
- MoleculeIteratorSinglet() - Constructor for class etomica.molecule.iterator.MoleculeIteratorSinglet
-
Constructs iterator without defining atom.
- MoleculeIteratorSinglet(IMolecule) - Constructor for class etomica.molecule.iterator.MoleculeIteratorSinglet
-
Constructs iterator specifying that it return the given atom.
- moleculeList - Variable in class etomica.action.IntegratorDimerApproach
-
- moleculeList - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- moleculeList - Variable in class etomica.molecule.MoleculeToMoleculeListSpecies
-
- moleculeList - Variable in class etomica.potential.EwaldSummation
-
- moleculeList - Variable in class etomica.potential.EwaldSumMolecules
-
- moleculeList - Variable in class etomica.virial.ClusterSumMultibody
-
- moleculeList - Variable in class etomica.virial.PotentialNonAdditive
-
- MoleculeListProperty - Class in etomica.meta.properties
-
Created by kofke on 7/24/17.
- MoleculeListProperty(Object, PropertyDescriptor) - Constructor for class etomica.meta.properties.MoleculeListProperty
-
- moleculeLists - Variable in class etomica.box.AtomSetAllMolecules
-
- moleculeLists - Variable in class etomica.box.Box
-
- MoleculeListWrapper - Class in etomica.molecule
-
AtomSet formed by wrapping an AtomArrayList.
- MoleculeListWrapper() - Constructor for class etomica.molecule.MoleculeListWrapper
-
Wraps a new atom array of the given length.
- MoleculeListWrapper(IMoleculeList) - Constructor for class etomica.molecule.MoleculeListWrapper
-
Makes a new instance holding the atoms in the given atom set.
- MoleculeListWrapper(MoleculeArrayList) - Constructor for class etomica.molecule.MoleculeListWrapper
-
Wraps the given atom array.
- MoleculeNeighborLists - Class in etomica.nbr.list.molecule
-
Class used to maintain neighbor lists.
- MoleculeNeighborLists() - Constructor for class etomica.nbr.list.molecule.MoleculeNeighborLists
-
Constructs sequencer for the given molecule.
- moleculeOffset - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- moleculeOffset - Variable in class etomica.modules.sam.ConfigurationSAM
-
- MoleculeOriented - Class in etomica.molecule
-
Molecule class appropriate for a rigid molecule.
- MoleculeOriented(Space, ISpecies, int) - Constructor for class etomica.molecule.MoleculeOriented
-
- MoleculeOriented(Space, ISpecies, int, boolean) - Constructor for class etomica.molecule.MoleculeOriented
-
- MoleculeOrientedDynamic - Class in etomica.molecule
-
Molecule class appropriate for a rigid molecule in a dynamic context.
- MoleculeOrientedDynamic(Space, ISpecies, int) - Constructor for class etomica.molecule.MoleculeOrientedDynamic
-
- moleculePair - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- MoleculePair - Class in etomica.molecule
-
Data structure that contains two mutable atom instances.
- MoleculePair() - Constructor for class etomica.molecule.MoleculePair
-
- MoleculePair(IMolecule, IMolecule) - Constructor for class etomica.molecule.MoleculePair
-
- moleculePair - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- MoleculePositionCOM - Class in etomica.molecule
-
Calculates the center of mass (COM) over a set of atoms.
- MoleculePositionCOM(Space) - Constructor for class etomica.molecule.MoleculePositionCOM
-
- MoleculePositionFirstAtom - Class in etomica.molecule
-
Returns the position of the first child leaf atom.
- MoleculePositionFirstAtom() - Constructor for class etomica.molecule.MoleculePositionFirstAtom
-
- MoleculePositionGeometricCenter - Class in etomica.molecule
-
Calculates the geometric center over a set of atoms.
- MoleculePositionGeometricCenter(Space) - Constructor for class etomica.molecule.MoleculePositionGeometricCenter
-
- MoleculePositionGeometricCenterAlkaneEH - Class in etomica.molecule
-
Calculates the geometric center over a set of atoms.
- MoleculePositionGeometricCenterAlkaneEH(Space, ISpecies) - Constructor for class etomica.molecule.MoleculePositionGeometricCenterAlkaneEH
-
- MoleculePositionGeometricCenterPBC - Class in etomica.molecule
-
Calculates the geometric center over a set of atoms.
- MoleculePositionGeometricCenterPBC(Space, Boundary) - Constructor for class etomica.molecule.MoleculePositionGeometricCenterPBC
-
- MoleculePotential1ListSource(PotentialMasterListMolecular) - Constructor for class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource
-
- MoleculePotentialList - Class in etomica.nbr.list.molecule
-
Class used to maintain list of whether each 1-body potential that
applies to a species is currently in effect or not for an Molecule.
- MoleculePotentialList() - Constructor for class etomica.nbr.list.molecule.MoleculePotentialList
-
Constructs sequencer for the given atom.
- moleculeRemoved(IMolecule) - Method in class etomica.box.BoxEventManager
-
- molecules - Variable in class etomica.normalmode.CoordinateDefinition.BasisCell
-
- molecules - Variable in class etomica.virial.ClusterWheatleyMultibody
-
- molecules - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
-
- molecules - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- molecules - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- molecules - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
-
- MoleculesetArray - Class in etomica.molecule
-
AtomSet formed by wrapping an Atom array.
- MoleculesetArray(int) - Constructor for class etomica.molecule.MoleculesetArray
-
Wraps a new atom array of the given length.
- MoleculesetArray(IMoleculeList) - Constructor for class etomica.molecule.MoleculesetArray
-
Makes a new instance holding the atoms in the given atom set.
- MoleculesetArray(MoleculesetArray) - Constructor for class etomica.molecule.MoleculesetArray
-
Copy constructor, wrapping a new array unique to this instance but
holding the same atoms as the given atom set.
- MoleculesetArray(IMolecule[]) - Constructor for class etomica.molecule.MoleculesetArray
-
Wraps the given atom array.
- MoleculesetIterator - Interface in etomica.molecule.iterator
-
Interface for classes that loop over a set of atoms.
- MoleculesetIteratorBasisDependent - Interface in etomica.molecule.iterator
-
Interface for an MoleculeIterator that can be conditioned with
target and basis molecules.
- MoleculesetIteratorBoxDependent - Interface in etomica.molecule.iterator
-
Interface indicating that an iterator can determine appropriate
atoms for iteration given an arbitrary box.
- MoleculesetIteratorCellular - Interface in etomica.nbr.cell.molecule
-
Interface for moleculeset iterators that use cell-based neighbor
lists for iteration.
- MoleculesetIteratorPDT - Interface in etomica.molecule.iterator
-
This is an interface for iterators that are box dependent, directable,
and targetable.
- MoleculesetIteratorTargetable - Interface in etomica.molecule.iterator
-
Interface for an iterator that can be targeted at one or more atoms.
- MoleculeSetSinglet - Class in etomica.molecule
-
Data structure that contains a single mutable atom instance.
- MoleculeSetSinglet() - Constructor for class etomica.molecule.MoleculeSetSinglet
-
- MoleculeSetSinglet(IMolecule) - Constructor for class etomica.molecule.MoleculeSetSinglet
-
- moleculeSetSinglet - Variable in class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
- moleculeSetSinglet - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- moleculeSetSinglet - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- moleculeSite - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- moleculeSite - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- moleculeSiteManager - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
-
- moleculeSiteManager - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- MoleculeSiteSource(Space, IMoleculePositionDefinition) - Constructor for class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource
-
- MoleculeSiteSource(Space, IMoleculePositionDefinition) - Constructor for class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
-
- moleculeSource - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- moleculeSource - Variable in class etomica.models.hexane.MCMoveCBMC
-
- moleculeSource - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- moleculeSource - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- moleculeSource - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- MoleculeSource - Interface in etomica.molecule
-
Interface for objects when return atoms (meeting some specification)
from a box.
- moleculeSource - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- moleculeSource - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- moleculeSource - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- moleculeSource - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- MoleculeSourceRandomDimer - Class in etomica.association
-
- MoleculeSourceRandomDimer() - Constructor for class etomica.association.MoleculeSourceRandomDimer
-
- MoleculeSourceRandomMolecule - Class in etomica.molecule
-
MoleculeSource that returns a completely random molecule.
- MoleculeSourceRandomMolecule() - Constructor for class etomica.molecule.MoleculeSourceRandomMolecule
-
- MoleculeSourceRandomMonomer - Class in etomica.association
-
- MoleculeSourceRandomMonomer() - Constructor for class etomica.association.MoleculeSourceRandomMonomer
-
- MoleculeToIndex - Interface in etomica.molecule
-
Interface for class that associates an integer with an atom.
- MoleculeToMoleculeList - Interface in etomica.molecule
-
Interface for class that determines an AtomArrayList given an atom.
- MoleculeToMoleculeListSpecies - Class in etomica.molecule
-
- MoleculeToMoleculeListSpecies(ISpecies) - Constructor for class etomica.molecule.MoleculeToMoleculeListSpecies
-
- MoleculeToMoleculeSetFixed - Class in etomica.molecule
-
- MoleculeToMoleculeSetFixed() - Constructor for class etomica.molecule.MoleculeToMoleculeSetFixed
-
- moleculeTotals - Variable in class etomica.box.AtomSetAllMolecules
-
- moleFractionLeft - Variable in class etomica.modules.osmosis.Osmosis
-
- moleFractionRight - Variable in class etomica.modules.osmosis.Osmosis
-
- molIndex - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- molIndex - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- molNum - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- molSpeciesA - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- molSpeciesB - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- moment - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- moment - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- moment - Variable in class etomica.modules.droplet.MeterDeformation
-
- moment - Variable in class etomica.modules.vle.VLESim
-
- moment - Static variable in class etomica.potential.P2NitrogenHellmann
-
- moment - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- moment - Variable in class etomica.species.SpeciesOriented
-
- moment - Variable in class etomica.species.SpeciesSpheresRotatingMolecule
-
- moment - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
-
- moment0 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- moment0 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- moment1 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- moment1 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- momentj - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- momentOfIntertia - Variable in class etomica.atom.AtomTypeOriented
-
- momentum - Variable in class etomica.action.BoxScaleMomenta
-
- momentum - Variable in class etomica.integrator.IntegratorMD
-
- Momentum - Class in etomica.units.dimensions
-
Dimension for all units of momentum, Mass-Length/Time
- monitorenergy - Static variable in class org.jmol.script.Token
-
- monomer1 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
-
- monomerA - Variable in class etomica.action.IntegratorDimerApproach
-
- monomerB - Variable in class etomica.action.IntegratorDimerApproach
-
- monomerColor - Variable in class etomica.association.ColorSchemeSmer
-
- monomerMonomerBondManager - Variable in class etomica.modules.colloid.ColloidSim
-
- monomerMonomerBondManager - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- monomerMonomerBondManager - Variable in class etomica.modules.colloid.P1Wall
-
- moreDefaultColors - Variable in class etomica.graphics.ColorSchemeByType
-
- MOST_RECENT - Static variable in class etomica.data.AccumulatorAverage
-
- MOST_RECENT - Static variable in class etomica.data.AccumulatorAverageBlockless
-
- mostRecent - Variable in class etomica.data.AccumulatorAverage
-
- mostRecent - Variable in class etomica.data.AccumulatorAverageBlockless
-
- mostRecentBlock - Variable in class etomica.data.AccumulatorAverageFixed
-
- mostRecentBlock - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- mostRecentValue - Variable in class etomica.normalmode.ModifierCells3D
-
- mostRecentValue - Variable in class etomica.normalmode.ModifierXCells2D
-
- mostRecentValue - Variable in class etomica.normalmode.ModifierYCells2D
-
- MOUSE_NONE - Static variable in class org.jmol.viewer.JmolConstants
-
- mouseClicked(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
-
- mouseClicked(MouseEvent) - Method in class etomica.util.Grabber.CornerSetListener
-
- mouseClicked(MouseEvent) - Method in class etomica.util.Grabber.DefaultMouseListener
-
- mousedragfactor - Static variable in class org.jmol.script.Token
-
- mouseEntered(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
-
- mouseEntered(MouseEvent) - Method in class etomica.util.Grabber.CornerSetListener
-
- mouseEntered(MouseEvent) - Method in class etomica.util.Grabber.DefaultMouseListener
-
- MouseEventClusterPanel() - Constructor for class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
-
- mouseExited(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
-
- mouseExited(MouseEvent) - Method in class etomica.util.Grabber.CornerSetListener
-
- mouseExited(MouseEvent) - Method in class etomica.util.Grabber.DefaultMouseListener
-
- mousePressed(MouseEvent) - Method in class etomica.graphics.DisplayPlot.PopupListener
-
- mousePressed(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
-
- mousePressed(MouseEvent) - Method in class etomica.util.Grabber.CornerSetListener
-
- mousePressed(MouseEvent) - Method in class etomica.util.Grabber.DefaultMouseListener
-
- mouseReleased(MouseEvent) - Method in class etomica.graphics.DisplayPlot.PopupListener
-
- mouseReleased(MouseEvent) - Method in class etomica.modules.clustergenerator.MyApplet.MouseEventClusterPanel
-
- mouseReleased(MouseEvent) - Method in class etomica.util.Grabber.CornerSetListener
-
- mouseReleased(MouseEvent) - Method in class etomica.util.Grabber.DefaultMouseListener
-
- mousewheelfactor - Static variable in class org.jmol.script.Token
-
- movable - Variable in class etomica.dimer.EnergyMap
-
- movable - Variable in class etomica.dimer.SimDimerLJadatom
-
- movable - Variable in class etomica.dimer.SimDimerLJgb
-
- movable - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- movable - Variable in class etomica.dimer.SimDimerMEAMGB
-
- movable - Variable in class etomica.kmc.SimKMCLJadatom
-
- movable - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- movableAtoms - Variable in class etomica.dimer.IntegratorDimerMin
-
- movableAtoms - Variable in class etomica.dimer.IntegratorDimerRT
-
- movableSet - Variable in class etomica.dimer.SimDimerLJadatom
-
- movableSet - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- movableSet - Variable in class etomica.dimer.SimDimerMEAMGB
-
- movableSet - Variable in class etomica.kmc.SimKMCLJadatom
-
- movableSet - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- movableSpecies - Variable in class etomica.dimer.IntegratorDimerMin
-
- movableSpecies - Variable in class etomica.dimer.IntegratorDimerRT
-
- move - Variable in class etomica.data.DataSourceAcceptanceRatio
-
- move - Variable in class etomica.mappedRdf.MappedRdf
-
- move - Variable in class etomica.mappedvirial.MappedU
-
- move - Variable in class etomica.mappedvirial.MappedVirialLJ
-
- move - Variable in class etomica.mappedvirial.MappedVirialLJVGr
-
- move - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- move - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- move - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- move - Variable in class etomica.modules.adsorption.ModifierPMu
-
- move - Variable in class etomica.normalmode.HessianDB
-
- move - Variable in class etomica.normalmode.SimOverlap
-
- move - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- move - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- move - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- move - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- move - Variable in class etomica.normalmode.SimUmbrella
-
- move - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- moveA - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- moveAction - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- moveB - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- moved - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- moveEventManager - Variable in class etomica.integrator.IntegratorMC
-
- moveHarmonic - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- moveManager - Variable in class etomica.integrator.IntegratorManagerMC
-
- moveManager - Variable in class etomica.integrator.IntegratorMC
-
- moveMolecule - Variable in class etomica.AlkaneEH.CH4NVT
-
- moveMolecule - Variable in class etomica.AlkaneEH.DHS_NVT
-
- moveMolecule - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
-
- moveMolecule - Variable in class etomica.dielectric.DHS_NVT
-
- moveMolecule - Variable in class etomica.dielectric.DLJ_NVT_1site
-
- moveMolecule - Variable in class etomica.dielectric.TIP4P_NVT
-
- moveMolecule - Variable in class etomica.models.hexane.HexaneVolumeFraction
-
- moveMolecule - Variable in class etomica.models.hexane.TestHexane
-
- moveMolecule - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- moveMolecule - Variable in class etomica.models.hexane.TestHexaneHarmonic
-
- moveMolecule - Variable in class etomica.models.hexane.TestSetToUHexane
-
- moveMoleculeAction - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- moveMoleculeAction - Variable in class etomica.association.BiasVolumeAceticAcid
-
- moveMoleculeAction - Variable in class etomica.association.MCMoveBiasUBMolecule
-
- moveMoleculeAction - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- moveMoleculeAction - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- moveMoleculeAction - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- moveMoleculeAction - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- moveMoleculeAction - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- moveMoleculeAction - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- moveTo(Vector) - Method in class etomica.math.geometry.Plane
-
Shifts the plane at fixed orientation so that it contains the given point.
- moveto - Static variable in class org.jmol.script.Token
-
- moveTracker - Variable in class etomica.integrator.mcmove.MCMove
-
- moveWallAction - Variable in class etomica.modules.sam.SamGraphic
-
- Mpi1ACell - Class in etomica.nbr.cell.molecule
-
Generates pairs that are cell-based neighbors of a specific Molecule.
- Mpi1ACell(int, double, BoxAgentManager) - Constructor for class etomica.nbr.cell.molecule.Mpi1ACell
-
Constructor makes iterator that must have box specified and then be
reset() before iteration.
- MpiAACell - Class in etomica.nbr.cell.molecule
-
Returns iterates formed from all cell-based neighbor pairs.
- MpiAACell(int, double, Box) - Constructor for class etomica.nbr.cell.molecule.MpiAACell
-
Constructor makes iterator that must have box specified and then be
reset() before iteration.
- MpiInnerFixed - Class in etomica.molecule.iterator
-
Pair iterator synthesized from two atom iterators, such that the inner-loop
iteration is independent of the outer-loop atom.
- MpiInnerFixed(MoleculeIterator, MoleculeIterator, boolean) - Constructor for class etomica.molecule.iterator.MpiInnerFixed
-
Construct a pair iterator using the given atom iterators, indicating
whether the atoms ordering in the AtomPair should be swapped from the
default behavior.
- MpiInnerVariable - Class in etomica.molecule.iterator
-
Pair iterator synthesized from two atom iterators, such that the inner-loop
iteration depends on the outer-loop atom.
- MpiInnerVariable(MoleculeIterator, MoleculeIteratorMoleculeDependent, boolean) - Constructor for class etomica.molecule.iterator.MpiInnerVariable
-
Construct a pair iterator using the given atom iterators, indicating
whether the atoms ordering in the AtomPair should be swapped from the
default behavior.
- MpiInterArrayList - Class in etomica.molecule.iterator
-
Returns all pairs formed from two different untabbed lists of molecules.
- MpiInterArrayList() - Constructor for class etomica.molecule.iterator.MpiInterArrayList
-
Construct iterator with an empty lists.
- MpiInterArrayList(IMoleculeList, IMoleculeList) - Constructor for class etomica.molecule.iterator.MpiInterArrayList
-
Constructs iterator to return pairs from the given lists.
- MpiInterspecies1A - Class in etomica.molecule.iterator
-
Gives pairs formed from the molecules of two different species in a box,
taking one molecule of one species with all molecules of the other.
- MpiInterspecies1A(ISpecies[]) - Constructor for class etomica.molecule.iterator.MpiInterspecies1A
-
Sorts given array of species according to species index, then constructs iterator
such that atom0 of the pair iterates is in (sorted) species[0], and atom1 is in
(sorted) species[1], regardless of which is specified via setTarget.
- MpiInterspeciesAA - Class in etomica.molecule.iterator
-
Gives pairs formed from the molecules of two different species in a box.
- MpiInterspeciesAA(ISpecies[]) - Constructor for class etomica.molecule.iterator.MpiInterspeciesAA
-
Constructs iterator that provides iterates taken from the molecules of
two species.
- MpiIntraArrayList - Class in etomica.molecule.iterator
-
Returns all pairs formed from a single list of molecules.
- MpiIntraArrayList() - Constructor for class etomica.molecule.iterator.MpiIntraArrayList
-
Construct iterator with an empty list.
- MpiIntraArrayList(IMoleculeList) - Constructor for class etomica.molecule.iterator.MpiIntraArrayList
-
Constructs iterator to return pairs from the given list.
- MpiIntraspecies1A - Class in etomica.molecule.iterator
-
Gives pairs formed from the molecules of a species in a box, taking one
molecule the species with all of its other molecules.
- MpiIntraspecies1A(ISpecies) - Constructor for class etomica.molecule.iterator.MpiIntraspecies1A
-
- MpiIntraspecies1A(ISpecies, MoleculeToMoleculeListSpecies) - Constructor for class etomica.molecule.iterator.MpiIntraspecies1A
-
- MpiIntraspeciesAA - Class in etomica.molecule.iterator
-
Gives pairs formed from the molecules of a single species in a box.
- MpiIntraspeciesAA(ISpecies) - Constructor for class etomica.molecule.iterator.MpiIntraspeciesAA
-
- MpiMolecule - Class in etomica.molecule.iterator
-
Adapater class that wraps three atomPair iterators, one suitable for
iterating over all molecule pairs in a box (AA), another suitable for
iterating over all molecule pairs formed with a target molecule (1A), and the
third suitable for iterating over a single molecule pair (11).
- MpiMolecule(MoleculesetIteratorPDT, MoleculesetIteratorBoxDependent) - Constructor for class etomica.molecule.iterator.MpiMolecule
-
Constructs iterator by wrapping three others.
- mReeHooverFactor - Variable in class etomica.virial.cluster.ClusterDiagram
-
- msdCalc(MeterMeanSquareDisplacement) - Method in class etomica.kmc.IntegratorKMCCluster
-
- MSDCoordWriter - Class in etomica.zeolite
-
- MSDCoordWriter(Space, String) - Constructor for class etomica.zeolite.MSDCoordWriter
-
- MSDProcessor - Class in etomica.zeolite
-
- MSDProcessor(Space, String, String) - Constructor for class etomica.zeolite.MSDProcessor
-
- mspMinus - Variable in class etomica.virial.PYGenerator.IteratorEF
-
- mspPlus - Variable in class etomica.virial.PYGenerator.IteratorEF
-
- mSquare - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- mSquare - Variable in class etomica.dielectric.TIP4P_NVT.Param
-
- mt - Variable in class etomica.util.random.RandomMersenneTwister
-
- mti - Variable in class etomica.util.random.RandomMersenneTwister
-
- mType - Variable in class etomica.models.water.SpeciesWater4P
-
- mType - Variable in class etomica.models.water.SpeciesWater4PCOM
-
- mType - Variable in class etomica.models.water.SpeciesWater4POriented
-
- mu - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- mu - Variable in class etomica.metastable.LJmuVT.LJMCParams
-
- mu - Variable in class etomica.models.co2.PNCO2GCPM
-
- mu - Variable in class etomica.models.co2.PNGCPM
-
- mu(double) - Method in class etomica.modules.adsorption.EOSSW
-
- mu(double) - Method in class etomica.modules.adsorption.EOSSWPatel
-
- mu(double) - Method in class etomica.modules.adsorption.VEOS3SW
-
- Mu - Class in etomica.modules.mu
-
- Mu(Space) - Constructor for class etomica.modules.mu.Mu
-
- mu - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
-
- mu - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- mu - Variable in class etomica.statmech.HardSphereSolid.EOSParams
-
- mu0 - Variable in class etomica.metastable.LJmuVT.LJMCParams
-
- Mu1Modulator() - Constructor for class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
-
- mu2 - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
-
- mu2 - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
-
- Mu2Modulator() - Constructor for class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
-
- MuDeltaEBond(Space, P2WaterTIP4PHardCore, VirialB2WaterTIP4P_DHS_difference.P2WaterDHS) - Constructor for class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.MuDeltaEBond
-
- MuFBond(Space, P2WaterTIP4PHardCore) - Constructor for class etomica.virial.simulations.VirialB3C1TIP4Pwater.MuFBond
-
- MuFGeneral - Class in etomica.virial
-
- MuFGeneral(double, IPotentialMolecular) - Constructor for class etomica.virial.MuFGeneral
-
- muForPressure(double) - Method in class etomica.modules.adsorption.EOSSW
-
- muForPressure(double) - Method in class etomica.modules.adsorption.EOSSWPatel
-
- muForPressure(double) - Method in class etomica.modules.adsorption.VEOS3SW
-
- MuGeneral - Class in etomica.virial
-
- MuGeneral(double, IPotentialMolecular) - Constructor for class etomica.virial.MuGeneral
-
- MuGraphic - Class in etomica.modules.mu
-
- MuGraphic(Mu, Space) - Constructor for class etomica.modules.mu.MuGraphic
-
- MuGraphic.Applet - Class in etomica.modules.mu
-
- MuGraphic.DataProcessorMu - Class in etomica.modules.mu
-
- MuGraphic.DataSinkExcludeOverlap - Class in etomica.modules.mu
-
- MuGraphic.ModifierAtomDiameter - Class in etomica.modules.mu
-
- MuGraphic.ModifierEpsilon - Class in etomica.modules.mu
-
- MuGraphic.ModifierLambda - Class in etomica.modules.mu
-
- muHistory - Variable in class etomica.modules.mu.MuGraphic.DataProcessorMu
-
- Mul - Class in etomica.graph.operations
-
- Mul() - Constructor for class etomica.graph.operations.Mul
-
- Mul(double[], double[]) - Static method in class etomica.virial.CalcFFT
-
- mul(Matrix3f) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to the result of multiplying itself with
matrix m1.
- mul(float) - Method in class org.jmol.util.Matrix4f
-
Multiplies each element of this matrix by a scalar.
- mul(Matrix4f) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to the result of multiplying itself with
matrix m1.
- mul(float) - Method in class org.jmol.util.Quaternion
-
- Mul.MulParameters - Class in etomica.graph.operations
-
- mul2(Matrix3f, Matrix3f) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to the result of multiplying the two argument
matrices together.
- mul2(Matrix4f, Matrix4f) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to the result of multiplying the two argument
matrices together.
- mulf(float) - Method in class org.jmol.util.Matrix3f
-
Multiplies each element of this matrix by a scalar.
- mulFlex - Variable in class etomica.graph.operations.BiComponentSubst
-
- mulFlex - Variable in class etomica.graph.operations.ComponentSubst
-
- mulFlex - Variable in class etomica.graph.operations.Unfactor
-
- MulFlexible - Class in etomica.graph.operations
-
Perform graph multiplication for flexible molecules.
- MulFlexible() - Constructor for class etomica.graph.operations.MulFlexible
-
- MulFlexible.MulFlexibleParameters - Class in etomica.graph.operations
-
- MulFlexibleParameters(char[], byte, byte, byte, boolean) - Constructor for class etomica.graph.operations.MulFlexible.MulFlexibleParameters
-
- mulParameters() - Method in class etomica.graph.operations.ConvParameters
-
- MulParameters(byte) - Constructor for class etomica.graph.operations.Mul.MulParameters
-
- mulQ(Quaternion) - Method in class org.jmol.util.Quaternion
-
- mulScalar - Variable in class etomica.graph.operations.BiComponentSubst
-
- mulScalar - Variable in class etomica.graph.operations.ComponentSubst
-
- MulScalar - Class in etomica.graph.operations
-
Multiply graphs by a scalar (coefficient)
- MulScalar() - Constructor for class etomica.graph.operations.MulScalar
-
- mulScalar - Variable in class etomica.virial.PYGenerator.IteratorEF
-
- MulScalarParameters - Class in etomica.graph.operations
-
- MulScalarParameters(int, int) - Constructor for class etomica.graph.operations.MulScalarParameters
-
- MulScalarParameters(Coefficient) - Constructor for class etomica.graph.operations.MulScalarParameters
-
- multGcdLcm(Ifactor, int) - Method in class etomica.veos.bigdecimal.Ifactor
-
Multiply with another positive integer.
- MultiBDcount - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- multibody - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- multibody - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- multibody - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- multibody - Variable in class etomica.virial.cluster.VirialDiagrams
-
- multibody - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- multibody - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- multibody - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- multibody - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- MULTIBOND_ALWAYS - Static variable in class org.jmol.viewer.JmolConstants
-
- MULTIBOND_NEVER - Static variable in class org.jmol.viewer.JmolConstants
-
- MULTIBOND_NOTSMALL - Static variable in class org.jmol.viewer.JmolConstants
-
- MULTIBOND_WIREFRAME - Static variable in class org.jmol.viewer.JmolConstants
-
- multiBonds - Variable in class etomica.virial.ClusterBondsNonAdditive
-
- Multiharmonic - Class in etomica.modules.multiharmonic
-
TODO To change the template for this generated type comment go to
Window - Preferences - Java - Code Style - Code Templates
- Multiharmonic() - Constructor for class etomica.modules.multiharmonic.Multiharmonic
-
- MultiharmonicGraphic - Class in etomica.modules.multiharmonic
-
- MultiharmonicGraphic(Multiharmonic, Space) - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphic
-
- MultiharmonicGraphic.Applet - Class in etomica.modules.multiharmonic
-
- MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic.mbar
-
- MultiharmonicGraphicMC(MultiharmonicMC, Space) - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
-
- MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic
-
- MultiharmonicGraphicMC(MultiharmonicMC, Space) - Constructor for class etomica.modules.multiharmonic.MultiharmonicGraphicMC
-
- MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicGraphicMC(MultiharmonicMC, Space) - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- MultiharmonicGraphicMC - Class in etomica.modules.multiharmonic.umbrella
-
- MultiharmonicGraphicMC(MultiharmonicMC, Space) - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
-
- MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic.mbar
-
- MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic
-
- MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicGraphicMC.Applet - Class in etomica.modules.multiharmonic.umbrella
-
- MultiharmonicGraphicMC.DataProcessAHT - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicGraphicMC.DataSinkReweightedDeltaU - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicGraphicMC.DataSourceAlphaAlpha - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicGraphicMC.DataSourceAlphaAlpha - Class in etomica.modules.multiharmonic.umbrella
-
- MultiharmonicGraphicMC.DataSourceAlphaChi - Class in etomica.modules.multiharmonic.mbar
-
- MultiharmonicGraphicMC.DataSourceAlphaChi - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicGraphicMC.DataSourceAlphaChi - Class in etomica.modules.multiharmonic.umbrella
-
- MultiharmonicGraphicMC.DataSourceAlphaFE - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicGraphicMC.DataSourceBias - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicGraphicMC.DataSourceChiSlope - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicGraphicMC.DataSourceFE - Class in etomica.modules.multiharmonic.mbar
-
- MultiharmonicGraphicMC.DataSourceFunctionRaw - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicGraphicMC.DataSourceUa - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicGraphicMC.DataSourceUa2 - Class in etomica.modules.multiharmonic.overlap
-
- MultiharmonicMC - Class in etomica.modules.multiharmonic.mbar
-
MC version of multi-harmonic simulation.
- MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- MultiharmonicMC - Class in etomica.modules.multiharmonic
-
MC version of multi-harmonic simulation.
- MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.MultiharmonicMC
-
- MultiharmonicMC - Class in etomica.modules.multiharmonic.overlap
-
MC version of multi-harmonic simulation.
- MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- MultiharmonicMC - Class in etomica.modules.multiharmonic.umbrella
-
MC version of multi-harmonic simulation.
- MultiharmonicMC() - Constructor for class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- multiP - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- multiplebondradiusfactor - Static variable in class org.jmol.script.Token
-
- multiplebondspacing - Static variable in class org.jmol.script.Token
-
- multiply(Coefficient) - Method in interface etomica.graph.model.Coefficient
-
- multiply(Coefficient) - Method in class etomica.graph.model.impl.CoefficientImpl
-
- multiply(BigInteger) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Multiply by a constant factor.
- multiply(BigIntegerPoly) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Multiply by another polynomial
- multiply(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurd
-
Multiply by another square root.
- multiply(Rational) - Method in class etomica.veos.bigdecimal.BigSurd
-
Multiply by a rational number.
- multiply(BigInteger) - Method in class etomica.veos.bigdecimal.BigSurd
-
Multiply by a BigInteger.
- multiply(int) - Method in class etomica.veos.bigdecimal.BigSurd
-
Multiply by an integer.
- multiply(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Multiply by another square root.
- multiply(BigInteger) - Method in class etomica.veos.bigdecimal.Ifactor
-
Multiply with another positive integer.
- multiply(int) - Method in class etomica.veos.bigdecimal.Ifactor
-
Multiply with another positive integer.
- multiply(Ifactor) - Method in class etomica.veos.bigdecimal.Ifactor
-
Multiply with another positive integer.
- multiply(Rational) - Method in class etomica.veos.bigdecimal.Rational
-
Multiply by another fraction.
- multiply(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
Multiply by a BigInteger.
- multiply(int) - Method in class etomica.veos.bigdecimal.Rational
-
Multiply by an integer.
- Multiply(Set<Graph>, Set<Graph>) - Static method in class etomica.virial.IEGenerator
-
- multiplyRound(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Multiply and round.
- multiplyRound(BigComplex, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Multiply and round.
- multiplyRound(BigComplex, BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Multiply and round.
- multiplyRound(BigDecimal, Rational) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Multiply and round.
- multiplyRound(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Multiply and round.
- multiplyRound(BigDecimal, BigInteger) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Multiply and round.
- multiprocessor - Static variable in class org.jmol.script.Token
-
- multiTol - Variable in class etomica.virial.ClusterWheatleyMultibody
-
- multiTol - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- MulUnion - Class in etomica.graph.operations
-
This operation multiplies two graphs (or each pair of graphs from two sets)
by superimposing all points (with the idea that all nodes are
distinguishable).
- MulUnion() - Constructor for class etomica.graph.operations.MulUnion
-
- mUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- mUnit - Variable in class etomica.modules.swmd.SwmdGraphic
-
- MuProduct(P2WaterTIP4PHardCore) - Constructor for class etomica.virial.simulations.VirialB3C2TIP4Pwater.MuProduct
-
- muProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- Mv1Squared(Vector) - Method in interface etomica.space.Vector
-
Returns square of vector resulting from subtracting given vector
from this one.
- Mv1Squared(Vector) - Method in class etomica.space1d.Vector1D
-
- Mv1Squared(Vector) - Method in class etomica.space2d.Vector2D
-
- Mv1Squared(Vector) - Method in class etomica.space3d.Vector3D
-
- Mv1Squared(Vector) - Method in class etomica.spaceNd.VectorND
-
- mxcBond - Variable in class etomica.virial.cluster.VirialDiagrams
-
- MxcBond - Variable in class etomica.virial.cluster.VirialDiagrams
-
- mxcBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- MxcBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- mxter - Static variable in class etomica.potential.P2O2Bartolomei
-
- myAcceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- myAcceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- myAcceptNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- MyAgent(Space) - Constructor for class etomica.integrator.IntegratorVelocityVerlet.MyAgent
-
- MyAgent(Space) - Constructor for class etomica.modules.droplet.IntegratorDroplet.MyAgent
-
- MyAgent(Space) - Constructor for class etomica.normalmode.HSNPT.MyAgent
-
- MyAgent(double, double) - Constructor for class etomica.potential.P3AxilrodTeller.MyAgent
-
- MyAgent(double[], Vector[], double[], Vector[]) - Constructor for class etomica.potential.P3Induction.MyAgent
-
- MyAgentSource(Space) - Constructor for class etomica.conjugategradient.DerivativeEnergyFunction.MyAgentSource
-
- MyAgentSource(Space) - Constructor for class etomica.conjugategradient.FiniteDifferenceDerivativeCG.MyAgentSource
-
- MyApplet - Class in etomica.modules.clustergenerator
-
- MyApplet() - Constructor for class etomica.modules.clustergenerator.MyApplet
-
- MyApplet.BondInteractionTypeToggler - Class in etomica.modules.clustergenerator
-
Options for type of bond-interaction (e-bonds, f-bonds, etc)
- MyApplet.BondTypeToggler - Class in etomica.modules.clustergenerator
-
Options for type of bond array
- MyApplet.ComponentEventMyPanel - Class in etomica.modules.clustergenerator
-
This class is to be notified to graphicOut2 when the window of applet is resized
- MyApplet.ConnectedToggler - Class in etomica.modules.clustergenerator
-
- MyApplet.GraphicsToggler - Class in etomica.modules.clustergenerator
-
- MyApplet.MouseEventClusterPanel - Class in etomica.modules.clustergenerator
-
This class is for showing bonds of selected cluster in GraphicPanel
- MyApplet.NumbersToggler - Class in etomica.modules.clustergenerator
-
Options for showing index of particle or not
- MyApplet.PointsToggler - Class in etomica.modules.clustergenerator
-
Option of showing particles or not
- MyApplet.ReeHooverToggler - Class in etomica.modules.clustergenerator
-
Options for type of bond-interaction (e-bonds, f-bonds, etc)
- MyApplet.Starter - Class in etomica.modules.clustergenerator
-
- MyApplet.Stopper - Class in etomica.modules.clustergenerator
-
- myAtom - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- myAtom - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- myAtoms - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- myAtoms - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- myAtoms - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- myAtoms - Variable in class etomica.virial.MCMoveClusterRingScale
-
- MyBigDecimal - Class in etomica.veos
-
Data class to handle operations involving large numbers.
- MyBigDecimal() - Constructor for class etomica.veos.MyBigDecimal
-
Default constructor sets value to 0.0
- MyBigDecimal(double) - Constructor for class etomica.veos.MyBigDecimal
-
Constructs using the given value.
- MyBigDecimal(IBigValue) - Constructor for class etomica.veos.MyBigDecimal
-
Copy constructor.
- MyBigDecimal(BigDecimal) - Constructor for class etomica.veos.MyBigDecimal
-
- myCharge - Variable in class etomica.models.water.ChargeAgentSourceTIP4PWater
-
- myCharge - Variable in class etomica.paracetamol.ChargeAgentSourceParacetamol
-
- MyCharge(double) - Constructor for class etomica.potential.EwaldSummation.MyCharge
-
- MyCharge(double) - Constructor for class etomica.potential.EwaldSumMolecules.MyCharge
-
- myData - Variable in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
-
- myData - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
-
- myData - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
-
- myData - Variable in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
-
- MyData() - Constructor for class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- MyData() - Constructor for class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- MyData(int) - Constructor for class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- MyDataCov(int) - Constructor for class etomica.virial.MeterVirialEBinMultiThreaded.MyDataCov
-
- MyEigenvalueDecomposition - Class in etomica.eigenstuff
-
Eigenvalues and eigenvectors of a real matrix.
- MyEigenvalueDecomposition(int, double[][]) - Constructor for class etomica.eigenstuff.MyEigenvalueDecomposition
-
Check for symmetry, then construct the eigenvalue decomposition
- myEllipse3D - Variable in class g3dsys.images.Ellipse
-
- MyForceTorque(Space) - Constructor for class etomica.action.ActionMinimizeEnergy.MyForceTorque
-
- MyFunctionInvertible(double) - Constructor for class etomica.modules.statistics.StatisticsMCGraphic.MyFunctionInvertible
-
- myIds - Static variable in class etomica.virial.cluster.VirialDiagrams
-
- myImage - Variable in class etomica.util.Grabber.ImagePanel
-
- myLat - Variable in class etomica.config.ConfigurationLattice
-
- myLat - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
- myLat - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
- MyLattice(SpaceLattice, Vector, Vector) - Constructor for class etomica.config.ConfigurationLattice.MyLattice
-
- MyLattice(SpaceLattice, Vector, Vector) - Constructor for class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
-
- MyLattice(SpaceLattice, Vector, Vector) - Constructor for class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
-
- myListener - Variable in class etomica.util.Grabber.ActionCornerSetter
-
- MyMCMove - Class in etomica.modules.adsorption
-
- MyMCMove(IntegratorBox, IRandom, Space, double, double, int) - Constructor for class etomica.modules.adsorption.MyMCMove
-
- MyMCMove - Class in etomica.modules.dcvgcmd
-
- MyMCMove(IntegratorBox, IRandom, Space, double) - Constructor for class etomica.modules.dcvgcmd.MyMCMove
-
- myMoleculeIndices - Variable in class etomica.virial.MayerFunctionThreeBody
-
- myPanel - Variable in class etomica.modules.clustergenerator.MyApplet
-
- myRejectNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- mySeeds - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- mySeeds - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- MySpeciesEditor(SpeciesSpheresMono, String) - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MySpeciesEditor
-
- mysum - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- MyTypeAgent(OrientationCalcQuaternion) - Constructor for class etomica.rotation.IntegratorVelocityVerletQuaternion.MyTypeAgent
-
- MyWall() - Constructor for class etomica.modules.osmosis.Osmosis.MyWall
-
N
- N - Variable in class etomica.dimer.IntegratorDimerMin
-
- N - Variable in class etomica.dimer.IntegratorDimerRT
-
- n - Variable in class etomica.graph.operations.DecorateWertheim2Site.DecorateWertheimParameters2Site
-
- n - Variable in class etomica.math.FactorialBenchmark
-
- n - Variable in class etomica.math.LnFactorialBenchmark
-
- N - Variable in class etomica.math.numerical.FittingFunctionNonLinear
-
- n - Variable in class etomica.math.numerical.PadeApproximation.VirialParam
-
- n - Variable in class etomica.meam.PotentialEAM
-
- n - Variable in class etomica.meam.PotentialEAM_LS
-
- n - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- N - Static variable in class etomica.potential.P3HydrogenManzhos
-
- n - Variable in class etomica.potential.P4TorsionDreiding
-
- N - Static variable in class etomica.util.random.RandomMersenneTwister
-
- n - Variable in class etomica.veos.bigdecimal.Ifactor
-
The standard representation of the number
- n - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
-
- N - Variable in class etomica.virial.CalcFFT
-
- n - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- n - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- n - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- n - Variable in class etomica.virial.cluster.VirialDiagrams
-
- n - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- n - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- n - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- n - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- n - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- n - Variable in class etomica.virial.ClusterChainHS
-
- n - Variable in class etomica.virial.ClusterChainSoft
-
- n - Variable in class etomica.virial.ClusterSinglyConnected
-
- n - Variable in class etomica.virial.ClusterSumHS
-
- n - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- n - Variable in class etomica.virial.ClusterWheatleyHS
-
- n - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
-
- n - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
-
- n - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- n - Variable in class etomica.virial.ClusterWheatleySoft
-
- n - Variable in class etomica.virial.ClusterWheatleySoftBD
-
- n - Variable in class etomica.virial.ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
-
- n - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- n - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
-
- n - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- n - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- n - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- n - Variable in class etomica.virial.MeterVirialSWWE
-
- n - Variable in class etomica.virial.simulations.ReeHooverMC.VirialParam
-
- n0 - Variable in class etomica.potential.P2HydrogenHinde
-
- n0 - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- n0 - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- n0 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- n0 - Variable in class etomica.potential.P2HydrogenPatkowski
-
- n0 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- N1 - Variable in class etomica.dimer.IntegratorDimerRT
-
- n1 - Variable in class etomica.graph.isomorphism.AbstractSearchState
-
- n1 - Variable in class etomica.potential.P2HydrogenHinde
-
- n1 - Variable in class etomica.potential.P2HydrogenHindeAtomic
-
- n1 - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- n1 - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- n1 - Variable in class etomica.potential.P2HydrogenPatkowski
-
- n1 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- n2 - Variable in class etomica.graph.isomorphism.AbstractSearchState
-
- n2 - Variable in class etomica.meam.P2EAM
-
- N_BASE - Static variable in class etomica.units.dimensions.Dimension
-
Number of base dimensions, equal to seven.
- n_max - Static variable in class etomica.potential.P2HydrogenPatkowski
-
- n_max - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- n_min - Static variable in class etomica.potential.P2HydrogenPatkowski
-
- n_min - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- nA - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- nA - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- nA - Variable in class etomica.normalmode.NormalModes1DHR
-
- Na - Static variable in class etomica.potential.P2QChemInterpolated
-
- naamax - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- nAccBlocks - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
-
- nAccBlocks - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- nAccBlocks - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- nAccept - Variable in class etomica.integrator.mcmove.MCMoveTracker
-
- nAccepted - Variable in class etomica.integrator.IntegratorMD
-
- nAccepted - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- nada - Static variable in class org.jmol.script.Token
-
- nAlpha - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- name - Variable in class etomica.compatibility.Feature
-
- name - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- nameOf(int) - Static method in class org.jmol.script.Token
-
note: nameOf is a very inefficient mechanism for getting
the name of a token.
- names - Static variable in class etomica.modules.joulethomson.JouleThomson.SpeciesChooser
-
- nand(Bitmap) - Method in interface etomica.graph.model.Bitmap
-
Updates this bitmap with the result of the bitwise AND with the other bitmap: bitmap
= ~(bitmap & other).
- nand(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- nand(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong
-
TIME = O(1) for a compatible instance.
- nand(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- nAtoms - Variable in class etomica.association.MCMoveVolumeAssociated.Agent
-
- nAtoms - Variable in class etomica.data.meter.MeterProfileByAtoms
-
- nAtoms - Variable in class etomica.modules.render.ParseObj
-
- nAtoms - Variable in class etomica.simulation.prototypes.HSMD3D.HSMD3DParam
-
Number of atoms, default = 256
- nAtomTypes - Variable in class etomica.models.co2.PNGCPM
-
- nAttempt - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- nAttempted - Variable in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- nAttempts - Variable in class etomica.integrator.mcmove.MCMoveAtomInRegion
-
- navfps - Static variable in class org.jmol.script.Token
-
- navigate - Static variable in class org.jmol.script.Token
-
- navigatesurface - Static variable in class org.jmol.script.Token
-
- navigationdepth - Static variable in class org.jmol.script.Token
-
- navigationmode - Static variable in class org.jmol.script.Token
-
- navigationperiodic - Static variable in class org.jmol.script.Token
-
- navigationslab - Static variable in class org.jmol.script.Token
-
- navigationspeed - Static variable in class org.jmol.script.Token
-
- navx - Static variable in class org.jmol.script.Token
-
- navy - Static variable in class org.jmol.script.Token
-
- NAVY - Static variable in class org.jmol.util.Colix
-
- navz - Static variable in class org.jmol.script.Token
-
- nBasis - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- nBasis - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- nBasis - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- nbbmax - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- nBeads - Variable in class etomica.virial.simulations.ModifierTPI
-
- nBeads - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- nBeads - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- nBeads - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- nBeads - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- nBeads - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- nBeads - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- nBeads - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- nBeads - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- nBeads - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- nbin - Static variable in class etomica.potential.P2O2Bartolomei
-
- nBins - Variable in class etomica.data.histogram.HistogramNotSoSimple
-
- nBins - Variable in class etomica.data.histogram.HistogramReweightedData
-
- nBins - Variable in class etomica.data.histogram.HistogramSimple
-
- nbins - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- nbins - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- nbins - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- nbins - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- nBins - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- nBins - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- nBins - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- nBins - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- nBins - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- nBins - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- nBlocks - Variable in class etomica.mappedRdf.MappedRdf.LJMDParams
-
- nBlocks - Variable in class etomica.mappedvirial.MappedU.LJMDParams
-
- nBlocks - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
-
- nBlocks - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
-
- nBody - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
-
- nBody - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
-
- nBody - Variable in class etomica.atom.iterator.ANIntergroupCoupled
-
- nBody() - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
- nBody() - Method in class etomica.atom.iterator.ANIntergroupExchange
-
- nBody - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- nBody() - Method in class etomica.atom.iterator.ANIntragroupExchange
-
- nBody() - Method in class etomica.atom.iterator.ApiIndexList
-
Returns 2, indicating that this is a pair iterator.
- nBody() - Method in class etomica.atom.iterator.ApiInnerVariable
-
- nBody() - Method in class etomica.atom.iterator.ApiInterArrayList
-
Returns 2, indicating that this is a pair iterator
- nBody() - Method in class etomica.atom.iterator.ApiIntergroup
-
- nBody() - Method in class etomica.atom.iterator.ApiIntraArrayList
-
Returns 2, indicating that this is a pair iterator
- nBody() - Method in class etomica.atom.iterator.ApiIntragroup
-
- nBody() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
- nBody() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
Returns 1, indicating that this is an atom AtomSet iterator.
- nBody() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Returns 1, indicating that this is an atom iterator.
- nBody() - Method in class etomica.atom.iterator.AtomIteratorNull
-
- nBody() - Method in class etomica.atom.iterator.AtomIteratorSinglet
-
- nBody() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
Returns 3, indicating that this is a set of three iterator.
- nBody() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
Returns 4, indicating that this is a set of four iterator.
- nBody() - Method in interface etomica.atom.iterator.AtomsetIterator
-
Returns the number of atoms given in each iterate, i.e., the
size of the atom array returned with each call to next().
- nBody() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
- nBody() - Method in class etomica.atom.iterator.TripletInnerSequential
-
- nBody() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- nBody() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- nBody() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- nBody() - Method in class etomica.models.co2.P2CO2H2OWheatley
-
- nBody() - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- nBody() - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- nBody() - Method in class etomica.models.co2.P2CO2Hellmann
-
- nBody() - Method in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- nBody() - Method in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- nBody() - Method in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- nBody() - Method in class etomica.models.co2.PNGCPM.PNGCPMCached
-
- nBody() - Method in class etomica.models.water.P2WaterSzalewicz
-
- nBody() - Method in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- nBody() - Method in class etomica.models.water.PNWaterGCPM.PNWaterGCPMCached
-
- nBody() - Method in class etomica.modules.adsorption.P1Wall
-
- nBody - Variable in class etomica.modules.clustergenerator.MyApplet
-
- nBody() - Method in class etomica.modules.colloid.P1Wall
-
- nBody() - Method in class etomica.modules.droplet.P1Smash
-
- nBody() - Method in class etomica.modules.materialfracture.P1Tension
-
- nBody() - Method in class etomica.modules.sam.P1Sinusoidal
-
- nBody() - Method in class etomica.molecule.iterator.MoleculeIteratorAll
-
- nBody() - Method in class etomica.molecule.iterator.MoleculeIteratorArrayListSimple
-
Returns 1, indicating that this is an atom iterator.
- nBody() - Method in class etomica.molecule.iterator.MoleculeIteratorSinglet
-
- nBody() - Method in class etomica.molecule.iterator.MpiInnerFixed
-
- nBody() - Method in class etomica.molecule.iterator.MpiInnerVariable
-
- nBody() - Method in class etomica.molecule.iterator.MpiInterArrayList
-
Returns 2, indicating that this is a pair iterator
- nBody() - Method in class etomica.molecule.iterator.MpiInterspecies1A
-
- nBody() - Method in class etomica.molecule.iterator.MpiInterspeciesAA
-
Returns 2, indicating that this is a pair iterator
- nBody() - Method in class etomica.molecule.iterator.MpiIntraArrayList
-
Returns 2, indicating that this is a pair iterator
- nBody() - Method in class etomica.molecule.iterator.MpiIntraspecies1A
-
- nBody() - Method in class etomica.molecule.iterator.MpiIntraspeciesAA
-
Returns 2, indicating that this is a pair iterator
- nBody() - Method in class etomica.molecule.iterator.MpiMolecule
-
Returns 2, indicating that this is a pair iterator.
- nBody() - Method in class etomica.nbr.cell.Api1ACell
-
Returns 2, indicating that this is a pair iterator.
- nBody() - Method in class etomica.nbr.cell.ApiAACell
-
Returns 2, indicating that this is a pair iterator.
- nBody() - Method in class etomica.nbr.cell.AtomIteratorCell
-
Returns 1, indicating that this is an atom iterator.
- nBody() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
Returns 1, indicating that this is an atom iterator.
- nBody() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
Returns 2, indicating that this is a pair iterator.
- nBody() - Method in class etomica.nbr.cell.molecule.MpiAACell
-
Returns 2, indicating that this is a pair iterator.
- nBody() - Method in class etomica.nbr.site.Api1ASite
-
Returns 2, indicating that this is a pair iterator.
- nBody() - Method in class etomica.normalmode.P1ConstraintNbr
-
- nBody() - Method in class etomica.normalmode.P1ConstraintNbrHcp
-
- nBody() - Method in class etomica.potential.EwaldSummation
-
- nBody() - Method in class etomica.potential.EwaldSummation.P2EwaldReal
-
- nBody() - Method in class etomica.potential.EwaldSumMolecules
-
- nBody() - Method in interface etomica.potential.IPotential
-
The number of atoms on which the potential depends.
- nBody() - Method in class etomica.potential.P1HardBoundary
-
- nBody() - Method in class etomica.potential.P1HydrogenMielke
-
- nBody() - Method in class etomica.potential.P1HydrogenMielke.P2HydrogenMielkeAtomic
-
- nBody() - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- nBody() - Method in class etomica.potential.P2EffectiveFeynmanHibbs
-
- nBody() - Method in class etomica.potential.P2HardWrapper
-
- nBody() - Method in class etomica.potential.P2HePCKLJS.P2HeQFH
-
- nBody() - Method in class etomica.potential.P2HePCKLJS.P2HeTI
-
- nBody() - Method in class etomica.potential.P2HeSimplified.P2HeQFH
-
- nBody() - Method in class etomica.potential.P2HeSimplified.P2HeTI
-
- nBody() - Method in class etomica.potential.P2HydrogenHinde
-
- nBody() - Method in class etomica.potential.P2HydrogenHindeAtomic
-
- nBody() - Method in class etomica.potential.P2HydrogenHindePatkowski
-
- nBody() - Method in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- nBody() - Method in class etomica.potential.P2HydrogenPatkowski
-
- nBody() - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- nBody() - Method in class etomica.potential.P2MoleculeMonatomic
-
- nBody() - Method in class etomica.potential.P2NitrogenHellmann
-
- nBody() - Method in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- nBody() - Method in class etomica.potential.P2O2Bartolomei
-
- nBody() - Method in class etomica.potential.P2O2Bartolomei.P2O2TI
-
- nBody() - Method in class etomica.potential.P2SemiclassicalAtomic
-
- nBody() - Method in class etomica.potential.P2SemiclassicalMolecular
-
- nBody() - Method in class etomica.potential.P2WaterPotentialsJankowski
-
- nBody() - Method in class etomica.potential.P3AxilrodTeller
-
- nBody() - Method in class etomica.potential.P3HydrogenATM
-
- nBody() - Method in class etomica.potential.P3HydrogenManzhos
-
- nBody() - Method in class etomica.potential.P3Induction
-
- nBody() - Method in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- nBody() - Method in class etomica.potential.Potential
-
The number of atoms on which the potential depends.
- nBody() - Method in class etomica.potential.PotentialAtomicSum
-
- nBody() - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- nBody() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- nBody - Variable in class etomica.potential.PotentialMolecular
-
- nBody() - Method in class etomica.potential.PotentialMolecular
-
The number of atoms on which the potential depends.
- nBody() - Method in class etomica.potential.PotentialMolecularSum
-
- nBody() - Method in class etomica.virial.P1IntraLambda
-
- nBody - Variable in class etomica.virial.PotentialCommonAtomic
-
- nBody() - Method in class etomica.virial.PotentialCommonAtomic
-
- nBody() - Method in class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
-
- nBody() - Method in class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
-
- nBody - Variable in class etomica.virial.PotentialNonAdditive
-
- nBody() - Method in class etomica.virial.PotentialNonAdditive
-
- nBody() - Method in class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
-
- nBody - Variable in class etomica.virial.simulations.VirialAceticAcid.VirialParam
-
- nBody - Variable in class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
-
- nBodyField - Variable in class etomica.modules.clustergenerator.MyApplet
-
- nBodyPretend - Variable in class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
-
- nbrDistance - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- nbrDistance - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- nbrList - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- nbrs - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- nbrVectors - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- nC - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- nC - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- nC - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- nC - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- nC - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- nC - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- nC - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- nC - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
-
- nC - Variable in class etomica.normalmode.NormalModesMolecular
-
- nC - Variable in class etomica.virial.ClusterChainHS
-
- nC - Variable in class etomica.virial.ClusterChainSoft
-
- nCell - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- nCell - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- nCell - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- nCell - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- nCellNum - Variable in class etomica.normalmode.NormalModes3D
-
- nCells - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- nCells - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- nCells - Variable in class etomica.normalmode.HessianDB
-
- nCells - Variable in class etomica.normalmode.LJVacancyMin
-
- nCells - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- nCells - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- nCells - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- nCells - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- nCells - Variable in class etomica.normalmode.SimBennet
-
- nCells - Variable in class etomica.normalmode.SimCalcSLJ
-
- nCells - Variable in class etomica.normalmode.SimCalcSMorse
-
- nCells - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
-
- nCells - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- nCells - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- nCells - Variable in class etomica.normalmode.SimEinStep1
-
- nCells - Variable in class etomica.normalmode.SimEinStep1HCP
-
- nCells - Variable in class etomica.normalmode.SimEinStep2
-
- nCells - Variable in class etomica.normalmode.SimEinStep2HCP
-
- nCells - Variable in class etomica.normalmode.SimHarmonic
-
- nCells - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- nCells - Variable in class etomica.normalmode.SimLJHTTISuper
-
- nCells - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- nCells - Variable in class etomica.normalmode.SimOverlap
-
- nCells - Variable in class etomica.normalmode.SimOverlapLJ
-
- nCells - Variable in class etomica.normalmode.SimOverlapLJModule
-
- nCells - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- nCells - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- nCells - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- nCells - Variable in class etomica.normalmode.SimTargetUmbrella
-
- nCells - Variable in class etomica.normalmode.SimUmbrella
-
- nCells - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- nCellsX - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- nCellsX - Variable in class etomica.modules.sam.ConfigurationSAM
-
- nCellsZ - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- nCellsZ - Variable in class etomica.modules.sam.ConfigurationSAM
-
- nci - Static variable in class org.jmol.script.Token
-
- nCO - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- nColumns - Variable in class etomica.graphics.DisplayTable
-
- nColumnsA - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- nComp1 - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
-
- nComp1 - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
-
- nComp2 - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
-
- nComp2 - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
-
- NCopy - Class in etomica.graph.operations
-
- NCopy() - Constructor for class etomica.graph.operations.NCopy
-
- nCrossLinkersAcid - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- nCutoffs - Variable in class etomica.liquidLJ.DataProcessorReweight
-
- nCutoffs - Variable in class etomica.liquidLJ.DataProcessorReweightRatio
-
- nData - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- nData - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- nData - Variable in class etomica.data.AccumulatorHistory
-
- nData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- nDataInfo - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- nDataInfo - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- nDataInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- nDataSource - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- NDelta - Variable in class etomica.dimer.IntegratorDimerMin
-
- NDelta - Variable in class etomica.dimer.IntegratorDimerRT
-
- nDer - Variable in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- nDer - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- nDer - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- nDer - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- nDer - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- nDer - Variable in class etomica.virial.simulations.VirialH2OGCPMD.VirialParam
-
- nDer - Variable in class etomica.virial.simulations.VirialLJD.VirialLJParam
-
- nDiAcid - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- nDimension() - Method in class etomica.units.dimensions.DimensionRatio
-
- nDiol - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- nEachIndices - Variable in class etomica.virial.cluster.PermutationIterator
-
- nEachIndicesCheck - Variable in class etomica.virial.cluster.PermutationIterator
-
- Near() - Constructor for class etomica.virial.MeterVirialExternalFieldSW.Near
-
- nearestImage(Vector) - Method in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
-
- nearestImage(Vector) - Method in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
-
- nearestImage(Vector) - Method in class etomica.space.Boundary
-
The nearest image is the pair of atom images that are closest when all
periodic-boundary images are considered.
- nearestImage(Vector) - Method in class etomica.space.BoundaryDeformablePeriodic
-
- nearestImage(Vector) - Method in class etomica.space.BoundaryRectangularNonperiodic
-
Does nothing.
- nearestImage(Vector) - Method in class etomica.space.BoundaryRectangularPeriodic
-
- nearestImage(Vector) - Method in class etomica.space.BoundaryRectangularPore
-
- nearestImage(Vector) - Method in class etomica.space.BoundaryRectangularSlit
-
- nearestImage(Vector) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
-
- needNeighborUpdate - Variable in class etomica.lattice.RectangularLatticeNbrIterator
-
- needSetupIterators - Variable in class etomica.atom.iterator.ANIntergroupCoupled
-
- needSetupIterators - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- needSetupIterators - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- needSetupIterators - Variable in class etomica.atom.iterator.ApiIntergroup
-
- needUpdate - Variable in class etomica.graphics.EtomicaPlot
-
- needUpdate(IAtom) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
-
- needUpdate(IAtom) - Method in class etomica.modules.render.RenderMD.CriterionCar
-
- needUpdate(IAtom) - Method in class etomica.modules.sam.CriterionTether3
-
- needUpdate(IAtom) - Method in class etomica.nbr.CriterionAdapter
-
Indicates whether the neighbor list for the given atom should be updated,
according to the wrapped criterion.
- needUpdate(IAtom) - Method in class etomica.nbr.CriterionAll
-
Always returns false, indicating that neighbor list never needs updating.
- needUpdate(IAtom) - Method in class etomica.nbr.CriterionNone
-
Always returns false, indicating that neighbor list never needs updating.
- needUpdate(IAtom) - Method in class etomica.nbr.CriterionPositionWall
-
- needUpdate(IAtom) - Method in class etomica.nbr.CriterionSimple
-
- needUpdate(IMolecule) - Method in class etomica.nbr.molecule.CriterionAdapterMolecular
-
Indicates whether the neighbor list for the given atom should be updated,
according to the wrapped criterion.
- needUpdate(IMolecule) - Method in class etomica.nbr.molecule.CriterionAllMolecular
-
Always returns false, indicating that neighbor list never needs updating.
- needUpdate(IMolecule) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- needUpdate(IMolecule) - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular
-
Indicates whether the neighbor list for the given molecule should
be updated, according to this criterion.
- needUpdate(IAtom) - Method in interface etomica.nbr.NeighborCriterion
-
Indicates whether the neighbor list for the given atom should
be updated, according to this criterion.
- Neff - Variable in class etomica.dimer.IntegratorDimerRT
-
- negate() - Method in class etomica.veos.bigdecimal.BigSurd
-
Compute the negative.
- negate() - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Compute the negative.
- negate() - Method in class etomica.veos.bigdecimal.Rational
-
Compute the negative.
- negate() - Method in class org.jmol.util.Quaternion
-
- negativeChop - Variable in class etomica.data.AccumulatorAverageBlockless
-
- negativeChop - Static variable in class etomica.data.AccumulatorAverageBlocklessSlim
-
- negativeChop - Variable in class etomica.data.AccumulatorAverageFixed
-
- negativeChop - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- negativeExchange - Variable in class etomica.virial.cluster.ExchangeSplit.ExchangeSplitParameters
-
- neighborAtoms - Variable in class etomica.normalmode.P1ConstraintNbr
-
- neighborAtoms - Variable in class etomica.normalmode.P1ConstraintNbrHcp
-
- neighborBonds(int) - Method in class etomica.modules.render.ParseObj
-
- NeighborCellManager - Class in etomica.nbr.cell
-
Class that defines and manages construction and use of lattice of cells
for cell-based neighbor listing.
- NeighborCellManager(Simulation, Box, double, Space) - Constructor for class etomica.nbr.cell.NeighborCellManager
-
Constructs manager for neighbor cells in the given box.
- NeighborCellManager(Simulation, Box, double, IMoleculePositionDefinition, Space) - Constructor for class etomica.nbr.cell.NeighborCellManager
-
Construct manager for neighbor cells in the given box.
- NeighborCellManagerList - Class in etomica.nbr.list
-
Subclass of NeighborCellManager that notifies the NeighborListManager when
an atom added to the box gets a cell.
- NeighborCellManagerList(Simulation, Box, double, Space) - Constructor for class etomica.nbr.list.NeighborCellManagerList
-
- NeighborCellManagerList(Simulation, Box, double, IMoleculePositionDefinition, Space) - Constructor for class etomica.nbr.list.NeighborCellManagerList
-
- NeighborCellManagerListMolecular - Class in etomica.nbr.list.molecule
-
Subclass of NeighborCellManager that notifies the NeighborListManager when
an atom added to the box gets a cell.
- NeighborCellManagerListMolecular(Simulation, Box, double, Space) - Constructor for class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
-
- NeighborCellManagerListMolecular(Simulation, Box, double, IMoleculePositionDefinition, Space) - Constructor for class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
-
- NeighborCellManagerMolecular - Class in etomica.nbr.cell.molecule
-
Class that defines and manages construction and use of lattice of cells
for cell-based neighbor listing.
- NeighborCellManagerMolecular(Simulation, Box, double, Space) - Constructor for class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Constructs manager for neighbor cells in the given box.
- NeighborCellManagerMolecular(Simulation, Box, double, IMoleculePositionDefinition, Space) - Constructor for class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Construct manager for neighbor cells in the given box.
- NeighborCellManagerThreaded - Class in etomica.threaded.domain
-
- NeighborCellManagerThreaded(Simulation, Box, double, Space) - Constructor for class etomica.threaded.domain.NeighborCellManagerThreaded
-
- NeighborCellManagerThreaded(Simulation, Box, double, IMoleculePositionDefinition, Space) - Constructor for class etomica.threaded.domain.NeighborCellManagerThreaded
-
- neighborCount - Variable in class etomica.lattice.RectangularLatticeNbrIterator
-
- NeighborCriterion - Interface in etomica.nbr
-
Atom filter used to specify whether two atoms are considered neighbors,
for the purpose of tabulating neighbor lists.
- NeighborCriterionMolecular - Interface in etomica.nbr.molecule
-
Atom filter used to specify whether two atoms are considered neighbors,
for the purpose of tabulating neighbor lists.
- neighborIterator - Variable in class etomica.association.MCMoveDimer
-
- neighborIterator - Variable in class etomica.association.MCMoveDimerRotate
-
- neighborIterator - Variable in class etomica.association.MCMoveSmer
-
- neighborIterator - Variable in class etomica.association.MCMoveSmerRotate
-
- neighborIterator - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- neighborIterator - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- NeighborIterator(int, double) - Constructor for class etomica.lattice.CellLattice.NeighborIterator
-
- neighborIterator - Variable in class etomica.nbr.site.PotentialMasterSite
-
- neighborListAgentManager - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- neighborListAgentManager - Variable in class etomica.nbr.list.PotentialMasterList
-
- neighborListAgentSource - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- neighborListAgentSource - Variable in class etomica.nbr.list.PotentialMasterList
-
- NeighborListAgentSource(double, Space) - Constructor for class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- NeighborListAgentSourceColloid(double, Space) - Constructor for class etomica.modules.colloid.NeighborListManagerColloid.NeighborListAgentSourceColloid
-
- NeighborListAgentSourceMolecular(double, Space) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- NeighborListAgentSourceThreaded(double, Space) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded.NeighborListAgentSourceThreaded
-
- NeighborListEventManager - Class in etomica.nbr.list
-
- NeighborListEventManager() - Constructor for class etomica.nbr.list.NeighborListEventManager
-
- NeighborListEventManagerMolecular - Class in etomica.nbr.list.molecule
-
- NeighborListEventManagerMolecular() - Constructor for class etomica.nbr.list.molecule.NeighborListEventManagerMolecular
-
- NeighborListManager - Class in etomica.nbr.list
-
Initiates the process of updating the neighbor lists.
- NeighborListManager(PotentialMasterList, double, Box, Space) - Constructor for class etomica.nbr.list.NeighborListManager
-
Configures instance for use by the given PotentialMaster.
- NeighborListManager.AtomPotential1ListSource - Class in etomica.nbr.list
-
- NeighborListManagerColloid - Class in etomica.modules.colloid
-
- NeighborListManagerColloid(PotentialMasterList, double, Box, Space) - Constructor for class etomica.modules.colloid.NeighborListManagerColloid
-
- NeighborListManagerColloid.NeighborListAgentSourceColloid - Class in etomica.modules.colloid
-
- NeighborListManagerMolecular - Class in etomica.nbr.list.molecule
-
Initiates the process of updating the neighbor lists.
- NeighborListManagerMolecular(PotentialMasterListMolecular, double, Box, Space) - Constructor for class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
Configures instance for use by the given PotentialMaster.
- NeighborListManagerMolecular.MoleculePotential1ListSource - Class in etomica.nbr.list.molecule
-
- NeighborListManagerSlanty - Class in etomica.nbr.list
-
Implements neighbor listing for a slanty box.
- NeighborListManagerSlanty(PotentialMasterList, double, Box, Space) - Constructor for class etomica.nbr.list.NeighborListManagerSlanty
-
Configures instance for use by the given PotentialMaster.
- NeighborListManagerSlanty.NeighborListSlantyAgentSource - Class in etomica.nbr.list
-
Constructs instances of NeighborListManagerSlanty on behalf of the
PotentialMaster
- NeighborListManagerSlantyMolecular - Class in etomica.nbr.list.molecule
-
Implements neighbor listing for a slanty box.
- NeighborListManagerSlantyMolecular(PotentialMasterListMolecular, double, Box, Space) - Constructor for class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular
-
Configures instance for use by the given PotentialMaster.
- NeighborListManagerSlantyMolecular.NeighborListSlantyAgentSourceMolecular - Class in etomica.nbr.list.molecule
-
Constructs instances of NeighborListManagerSlanty on behalf of the
PotentialMaster
- NeighborListManagerThreaded - Class in etomica.threaded.domain
-
- NeighborListManagerThreaded(PotentialMasterListThreaded, double, Box, Space) - Constructor for class etomica.threaded.domain.NeighborListManagerThreaded
-
- neighborListNeighborsUpdated() - Method in class etomica.integrator.IntegratorHard
-
- neighborListNeighborsUpdated() - Method in interface etomica.nbr.list.INeighborListListener
-
- neighborListNeighborsUpdated() - Method in interface etomica.nbr.list.molecule.INeighborListListenerMolecular
-
- neighborLists - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- neighborLists - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- NeighborListSlantyAgentSource(double, Space) - Constructor for class etomica.nbr.list.NeighborListManagerSlanty.NeighborListSlantyAgentSource
-
- NeighborListSlantyAgentSourceMolecular(double, Space) - Constructor for class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular.NeighborListSlantyAgentSourceMolecular
-
- neighborManager - Variable in class etomica.graphics.ColorSchemeOverlap
-
- neighborManager - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- neighborManager - Variable in class etomica.modules.mu.P1MagicWall
-
- neighborManager - Variable in class etomica.normalmode.MeterMaxExpansion
-
- neighborManager - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- neighborManager - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- neighborRadius2 - Variable in class etomica.nbr.CriterionSimple
-
- neighborRadius2 - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- neighborRadiusSq - Variable in class etomica.normalmode.P1ConstraintNbr
-
- neighborRadiusSq - Variable in class etomica.normalmode.P1ConstraintNbrHcp
-
- neighbors - Variable in class etomica.lattice.RectangularLatticeNbrIterator
-
- neighbors(int) - Method in class etomica.modules.render.ParseObj
-
- neighborSetup() - Method in class etomica.modules.colloid.NeighborListManagerColloid
-
- neighborSetup() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
Reassigns all interacting atoms to cells, then loops over all cell-list
neighbor pairs, determines for each pair whether a potential applies to it,
and if so, puts each in the other's neighbor list.
- neighborSetup() - Method in class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular
-
Reassigns all interacting atoms to cells, then loops over all atom
pairs, determines for each pair whether a potential applies to it,
and if so, puts each in the other's neighbor list.
- neighborSetup() - Method in class etomica.nbr.list.NeighborListManager
-
Reassigns all interacting atoms to cells, then loops over all cell-list
neighbor pairs, determines for each pair whether a potential applies to it,
and if so, puts each in the other's neighbor list.
- neighborSetup() - Method in class etomica.nbr.list.NeighborListManagerSlanty
-
Reassigns all interacting atoms to cells, then loops over all atom
pairs, determines for each pair whether a potential applies to it,
and if so, puts each in the other's neighbor list.
- neighborSetup() - Method in class etomica.threaded.domain.NeighborListManagerThreaded
-
- NeighborSiteManager - Class in etomica.nbr.site
-
Neighbor manager for system in which there is an unchanging, one-to-one
correspondence between atoms and lattice cells.
- NeighborSiteManager(Box, int) - Constructor for class etomica.nbr.site.NeighborSiteManager
-
Constructs manager for neighbor cells in the given box.
- neighborsUpdated() - Method in class etomica.nbr.list.molecule.NeighborListEventManagerMolecular
-
- neighborsUpdated() - Method in class etomica.nbr.list.NeighborListEventManager
-
- nEthane - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
-
- nEthane - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
-
- new3(float, float, float) - Static method in class org.jmol.util.Point3f
-
- new3(int, int, int) - Static method in class org.jmol.util.Point3i
-
- new3(float, float, float) - Static method in class org.jmol.util.Vector3f
-
- new4(float, float, float, float) - Static method in class org.jmol.util.AxisAngle4f
-
Constructs and initializes an AxisAngle4f from the specified x, y, z, and
angle.
- new4(float, float, float, float) - Static method in class org.jmol.util.Point4f
-
- new4(float, float, float, float) - Static method in class org.jmol.util.Quaternion
-
- newA(float[]) - Static method in class org.jmol.util.Matrix3f
-
Constructs and initializes a Matrix3f from the specified 9 element array.
- newA(float[]) - Static method in class org.jmol.util.Matrix4f
-
Constructs and initializes a Matrix4f from the specified 16 element array.
- newAA(AxisAngle4f) - Static method in class org.jmol.util.AxisAngle4f
-
Constructs and initializes a AxisAngle4f from the specified AxisAngle4f.
- newAA(AxisAngle4f) - Static method in class org.jmol.util.Quaternion
-
- newAndSetBit(int) - Static method in class org.jmol.util.BitSetUtil
-
- newAntialiasing - Variable in class org.jmol.util.GData
-
- newBitSet(int) - Static method in class org.jmol.util.BitSetUtil
-
- newBitSet2(int, int) - Static method in class org.jmol.util.BitSetUtil
-
- newBufferedImage(Object, int, int) - Method in interface org.jmol.api.ApiPlatform
-
- newBufferedImage(Object, int, int) - Method in class org.jmol.awt.Platform
-
- newByte2(int) - Static method in class org.jmol.util.ArrayUtil
-
- newColor0 - Variable in class etomica.graph.operations.SplitOne.SplitOneParameters
-
- newColor0() - Method in class etomica.graph.operations.SplitParameters
-
- newColor1 - Variable in class etomica.graph.operations.SplitOne.SplitOneParameters
-
- newColor1() - Method in class etomica.graph.operations.SplitParameters
-
- newData - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- newFloat2(int) - Static method in class org.jmol.util.ArrayUtil
-
- newFloat3(int, int) - Static method in class org.jmol.util.ArrayUtil
-
- newFont(String, boolean, boolean, float) - Method in interface org.jmol.api.ApiPlatform
-
- newFont(String, boolean, boolean, float) - Method in class org.jmol.awt.Platform
-
- newGeo - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- newI(int) - Static method in class org.jmol.util.Rgb16
-
- newInt2(int) - Static method in class org.jmol.util.ArrayUtil
-
- newInt4(int) - Static method in class org.jmol.util.ArrayUtil
-
- newLnA - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- newLnA - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- newM(double[][]) - Static method in class org.jmol.util.Eigen
-
- newM(Matrix3f) - Static method in class org.jmol.util.Matrix3f
-
Constructs a new matrix with the same values as the Matrix3f parameter.
- newM(Matrix4f) - Static method in class org.jmol.util.Matrix4f
-
Constructs a new matrix with the same values as the Matrix4f parameter.
- newM(Matrix3f) - Static method in class org.jmol.util.Quaternion
-
- newMesh(boolean, Tuple3f[], int, int[][], Tuple3f[], int) - Static method in class org.jmol.util.MeshSurface
-
- newMV(Matrix3f, Vector3f) - Static method in class org.jmol.util.Matrix4f
-
Constructs and initializes a Matrix4f from the rotation matrix
and translation.
- newN(int) - Static method in class org.jmol.util.BitSet
-
Creates a bit set whose initial size is large enough to explicitly
represent bits with indices in the range 0 through nbits-1.
- newN(int) - Static method in class org.jmol.util.StringXBuilder
-
- newOffScreenImage(int, int) - Method in interface org.jmol.api.ApiPlatform
-
- newOffScreenImage(int, int) - Method in class org.jmol.awt.Platform
-
- newOriginB - Variable in class etomica.action.IntegratorDimerApproach
-
- newP(Tuple3f) - Static method in class org.jmol.util.Point3f
-
- newP4(Point4f) - Static method in class org.jmol.util.Quaternion
-
- newPartners - Variable in class etomica.potential.PotentialReactive.BondChangeData
-
- newPosition - Variable in class etomica.dimer.IntegratorDimerRT
-
- newPositionC - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- newPositionC - Variable in class etomica.association.BiasVolumeAceticAcid
-
- newPt(Point4f) - Static method in class org.jmol.util.Point4f
-
- newQ(Quaternion) - Static method in class org.jmol.util.Quaternion
-
- newR - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
-
- newS(String) - Static method in class org.jmol.util.StringXBuilder
-
- newScriptVariableBs(BitSet, int) - Static method in class org.jmol.script.ScriptVariable
-
- newScriptVariableIntValue(int, int, Object) - Static method in class org.jmol.script.ScriptVariable
-
- newScriptVariableToken(Token) - Static method in class org.jmol.script.ScriptVariable
-
- newSeeds - Variable in class etomica.virial.simulations.SimulationVirial
-
- newShort2(int) - Static method in class org.jmol.util.ArrayUtil
-
- newSlab(Point3f[], int, float[], int[][], int, int) - Static method in class org.jmol.util.MeshSurface
-
- newSmerList - Variable in class etomica.association.MCMoveSmer
-
- newSmerList - Variable in class etomica.association.MCMoveSmerRotate
-
- newToken(int, int) - Static method in class org.jmol.script.Token
-
- newTokenIntVal(int, int, Object) - Static method in class org.jmol.script.Token
-
- newTokenObj(int, Object) - Static method in class org.jmol.script.Token
-
- Newton - Class in etomica.units
-
The Newton unit of force, equal to 1 kg-m/s^2.
- NewtonMinimization - Class in etomica.math.numerical
-
- NewtonMinimization(FunctionMultiDimensionalDifferentiable, boolean) - Constructor for class etomica.math.numerical.NewtonMinimization
-
- newtonRaphson(double, int, double, double, P1IntraMolecular) - Static method in class etomica.virial.simulations.VirialH2PIXC
-
- newTotalCosTheta - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- newU - Variable in class etomica.models.nitrogen.MeterDirectInitPert
-
- newU - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- newU - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- newV(Tuple3f) - Static method in class org.jmol.util.Vector3f
-
- newVA(Vector3f, float) - Static method in class org.jmol.util.AxisAngle4f
-
Constructs and initializes an AxisAngle4f from the specified axis and
angle.
- newVA(Tuple3f, float) - Static method in class org.jmol.util.Quaternion
-
- newValue - Variable in class etomica.server.representations.PropertyUpdate
-
- newVariable(int, Object) - Static method in class org.jmol.script.ScriptVariable
-
- newVertexBitSet() - Static method in class org.jmol.util.Normix
-
- newWindowHeight - Variable in class org.jmol.util.GData
-
- newWindowWidth - Variable in class org.jmol.util.GData
-
- nex - Static variable in class etomica.potential.P2HydrogenPatkowski
-
- nex - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- NexpStretchFit - Static variable in class etomica.statmech.HardSphereFluid
-
- NexpVirial - Static variable in class etomica.statmech.HardSphereFluid
-
- next() - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
- next() - Method in class etomica.atom.iterator.ANIntergroupExchange
-
- next() - Method in class etomica.atom.iterator.ANIntragroupExchange
-
- next() - Method in class etomica.atom.iterator.ApiIndexList
-
Returns the iterator's pair and unsets iterator.
- next() - Method in class etomica.atom.iterator.ApiInnerVariable
-
Returns the next pair of atoms.
- next() - Method in class etomica.atom.iterator.ApiInterArrayList
-
Returns the next iterate pair.
- next() - Method in class etomica.atom.iterator.ApiIntergroup
-
Returns the next pair of atoms.
- next() - Method in class etomica.atom.iterator.ApiIntergroupCoupled
-
Returns the next pair of atoms.
- next() - Method in class etomica.atom.iterator.ApiIntergroupExchange
-
Returns the next pair of atoms.
- next() - Method in class etomica.atom.iterator.ApiIntergroupIntraSpecies
-
Returns the next pair of atoms.
- next() - Method in class etomica.atom.iterator.ApiIntraArrayList
-
Returns the next iterate pair.
- next() - Method in class etomica.atom.iterator.ApiIntragroup
-
- next() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
- next() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
Same as nextAtom.
- next() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Same as nextAtom().
- next() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType
-
- next() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType2
-
- next() - Method in class etomica.atom.iterator.AtomIteratorLeafFilteredType
-
- next() - Method in class etomica.atom.iterator.AtomIteratorNull
-
- next() - Method in class etomica.atom.iterator.AtomIteratorSinglet
-
- next() - Method in interface etomica.atom.iterator.AtomLeafsetIterator
-
Returns the next AtomSet iterate, or null if hasNext() is false.
- next() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
Same as nextSet().
- next() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
- next() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
- next - Variable in class etomica.atom.iterator.TripletInnerSequential
-
- next() - Method in class etomica.atom.iterator.TripletInnerSequential
-
- next() - Method in class etomica.graph.iterators.CartesianIterator
-
- next() - Method in class etomica.graph.iterators.CartesianPermutator
-
- next() - Method in class etomica.graph.iterators.ChainedIterator
-
- next() - Method in class etomica.graph.iterators.DefaultIterator
-
- next() - Method in class etomica.graph.iterators.DefaultPermutator
-
- next() - Method in class etomica.graph.iterators.EdgelessIterator
-
- next() - Method in class etomica.graph.iterators.filters.GlobalFilter
-
- next() - Method in class etomica.graph.iterators.filters.LocalFilter
-
- next() - Method in class etomica.graph.iterators.FixedEdgeCountIterator
-
- next() - Method in class etomica.graph.iterators.IteratorWrapper
-
- next() - Method in class etomica.graph.iterators.RangePermutator
-
- next() - Method in class etomica.graph.iterators.StoredIterator
-
- next() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- next() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- next() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- next() - Method in interface etomica.lattice.IndexIterator
-
- next - Variable in class etomica.lattice.IndexIteratorIncreasing
-
- next() - Method in class etomica.lattice.IndexIteratorIncreasing
-
Returns the next index.
- next() - Method in class etomica.lattice.IndexIteratorRectangular
-
Returns the next iterate, or null if hasNext is false.
- next() - Method in class etomica.lattice.IndexIteratorReflecting
-
- next() - Method in class etomica.lattice.IndexIteratorTriangular
-
Returns the next iterate.
- next() - Method in class etomica.lattice.IndexIteratorTriangularPermutations
-
- next() - Method in class etomica.lattice.RectangularLattice.Iterator
-
- next() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Returns the next site in the iteration sequence, or null
if hasNext is false.
- next() - Method in interface etomica.lattice.SiteIterator
-
Returns the next iterate.
- next() - Method in class etomica.math.discrete.CombinationIterator
-
- next() - Method in class etomica.math.discrete.FixedSumIterator
-
- next() - Method in class etomica.math.discrete.PermutationDegenerateIterator
-
Returns the next iterate, or null if hasNext is false.
- next() - Method in class etomica.math.discrete.PermutationIterator
-
- next - Variable in class etomica.math.function.FunctionChain.Link
-
- next() - Method in class etomica.modules.pistoncylinder.ApiFilteredCylinder
-
- next - Variable in class etomica.molecule.iterator.MoleculeIteratorAll
-
- next() - Method in class etomica.molecule.iterator.MoleculeIteratorAll
-
- next() - Method in class etomica.molecule.iterator.MoleculeIteratorArrayListSimple
-
Same as nextAtom().
- next() - Method in class etomica.molecule.iterator.MoleculeIteratorSinglet
-
- next() - Method in interface etomica.molecule.iterator.MoleculesetIterator
-
Returns the next AtomSet iterate, or null if hasNext() is false.
- next() - Method in class etomica.molecule.iterator.MpiInnerFixed
-
Returns the next pair of atoms.
- next() - Method in class etomica.molecule.iterator.MpiInnerVariable
-
Returns the next pair of atoms.
- next() - Method in class etomica.molecule.iterator.MpiInterArrayList
-
Returns the next iterate pair.
- next() - Method in class etomica.molecule.iterator.MpiInterspecies1A
-
- next() - Method in class etomica.molecule.iterator.MpiInterspeciesAA
-
Returns the next iterate pair.
- next() - Method in class etomica.molecule.iterator.MpiIntraArrayList
-
Returns the next iterate pair.
- next() - Method in class etomica.molecule.iterator.MpiIntraspecies1A
-
- next() - Method in class etomica.molecule.iterator.MpiIntraspeciesAA
-
Returns the next iterate pair.
- next() - Method in class etomica.molecule.iterator.MpiMolecule
-
Same as nextPair.
- next() - Method in class etomica.nbr.cell.Api1ACell
-
- next() - Method in class etomica.nbr.cell.AtomIteratorCell
-
- next() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
- next() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
- next() - Method in class etomica.nbr.site.Api1ASite
-
- next - Variable in class etomica.potential.PotentialGroup.PotentialLinker
-
- next() - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- next() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- next() - Method in class etomica.virial.cluster.PermutationIterator
-
- next() - Method in class etomica.virial.PYGenerator.IteratorEF
-
- next() - Method in interface g3dsys.control.IndexIterator
-
Get the next set of indices
- next - Static variable in class org.jmol.script.Token
-
- nextAtom - Variable in class etomica.association.MCMoveVolumeAssociated.Agent
-
- nextAtom() - Method in interface etomica.atom.iterator.AtomIterator
-
Returns the next atom in the iteration sequence, or
null if hasNext() is false.
- nextAtom() - Method in class etomica.atom.iterator.AtomIteratorArrayList
-
Returns the next iterate and advances the iterator.
- nextAtom() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
Returns the next iterator, or null if hasNext is false.
- nextAtom() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Returns the next iterate and advances the iterator.
- nextAtom() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType
-
- nextAtom() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType2
-
- nextAtom() - Method in class etomica.atom.iterator.AtomIteratorLeafFilteredType
-
- nextAtom() - Method in class etomica.atom.iterator.AtomIteratorNull
-
- nextAtom() - Method in class etomica.atom.iterator.AtomIteratorSinglet
-
Returns the iterator's atom and unsets iterator.
- nextAtom() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- nextAtom() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- nextAtom() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- nextAtom() - Method in class etomica.nbr.cell.AtomIteratorCell
-
- nextClearBit(int) - Method in class org.jmol.util.BitSet
-
Returns the index of the first bit that is set to false that occurs
on or after the specified starting index.
- nextCursor - Variable in class etomica.molecule.iterator.MoleculeIteratorAll
-
- nextDouble() - Method in interface etomica.util.random.IRandom
-
Returns a pseudorandom double, uniformly distributed between
0.0 (exclusive) and 1.0 (exclusive).
- nextDouble() - Method in class etomica.util.random.RandomMersenneTwister
-
- nextDouble() - Method in class etomica.util.random.RandomNumberGenerator
-
- nextDouble() - Method in class etomica.util.random.RandomNumberGeneratorUnix
-
Returns a random double, uniformly distributed between 0 and 1.
- nextFixedDouble() - Method in interface etomica.util.random.IRandom
-
Returns a pseudorandom double, uniformly distributed between
0.0 (inclusive) and 1.0 (exclusive).
- nextFixedDouble() - Method in class etomica.util.random.RandomMersenneTwister
-
- nextFixedDouble() - Method in class etomica.util.random.RandomNumberGenerator
-
- nextFixedDouble() - Method in class etomica.util.random.RandomNumberGeneratorUnix
-
- nextFloat() - Method in class etomica.util.random.RandomMersenneTwister
-
- nextFloat() - Method in class etomica.util.random.RandomNumberGeneratorUnix
-
Returns a random float, uniformly distributed between 0 and 1.
- nextGaussian() - Method in interface etomica.util.random.IRandom
-
Returns a pseudorandom double, Gaussian ("normally") distributed
value with mean 0.0 and standard deviation 1.0.
- nextGaussian - Variable in class etomica.util.random.RandomMersenneTwister
-
- nextGaussian() - Method in class etomica.util.random.RandomMersenneTwister
-
- nextGaussian() - Method in class etomica.util.random.RandomNumberGenerator
-
- nextGaussian - Variable in class etomica.util.random.RandomNumberGeneratorUnix
-
- nextGaussian() - Method in class etomica.util.random.RandomNumberGeneratorUnix
-
Returns a double taken from a Gaussian distribution with 0 mean and
variance of 1.
- nextIndex() - Method in class etomica.lattice.RectangularLattice.Iterator
-
- nextIndex() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Returns the index of the next iterate while advancing the
iterator.
- nextIndex() - Method in interface etomica.lattice.SiteIterator
-
Returns the index of the next iterate while advancing iterator.
- nextInt(int) - Method in interface etomica.util.random.IRandom
-
Returns a pseudorandom integer, uniformly distributed between
0 (inclusive) and maxInt (exclusive).
- nextInt() - Method in class etomica.util.random.RandomMersenneTwister
-
- nextInt(int) - Method in class etomica.util.random.RandomMersenneTwister
-
Returns a random int ranging from 0 to max-1.
- nextInt(int) - Method in class etomica.util.random.RandomNumberGenerator
-
- nextInt() - Method in class etomica.util.random.RandomNumberGeneratorUnix
-
Returns a random int (32-bit integer).
- nextInt(int) - Method in class etomica.util.random.RandomNumberGeneratorUnix
-
Returns a random int ranging from 0 to max-1.
- nextLeft - Variable in class etomica.util.TreeLinker
-
- nextLong() - Method in class etomica.util.random.RandomMersenneTwister
-
- nextLong() - Method in class etomica.util.random.RandomNumberGeneratorUnix
-
Returns a random long (64-bit integer).
- nextLong(long) - Method in class etomica.util.random.RandomNumberGeneratorUnix
-
Returns a random long ranging from 0 to max-1.
- nextMolecule - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule.Agent
-
- nextMolecule() - Method in interface etomica.molecule.iterator.MoleculeIterator
-
Returns the next atom in the iteration sequence, or
null if hasNext() is false.
- nextMolecule() - Method in class etomica.molecule.iterator.MoleculeIteratorArrayList
-
Returns the next iterate and advances the iterator.
- nextMolecule() - Method in class etomica.molecule.iterator.MoleculeIteratorArrayListSimple
-
Returns the next iterate and advances the iterator.
- nextMolecule() - Method in class etomica.molecule.iterator.MoleculeIteratorSinglet
-
Returns the iterator's atom and unsets iterator.
- nextMolecule() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
- nextOp - Variable in class etomica.graph.operations.UnaryChain
-
- nextPair(NodePair) - Method in interface etomica.graph.isomorphism.SearchState
-
- nextPair(NodePair) - Method in class etomica.graph.isomorphism.UllmanSearchState
-
- nextPair(NodePair) - Method in class etomica.graph.isomorphism.VF2SearchState
-
- nextPair(NodePair) - Method in class etomica.graph.isomorphism.VFSearchState
-
- nextPair() - Method in class etomica.nbr.cell.ApiAACell
-
- nextPair() - Method in class etomica.nbr.cell.molecule.MpiAACell
-
- nextParams - Variable in class etomica.graph.operations.UnaryChain.ChainParameters
-
- nextprime(BigInteger) - Method in class etomica.veos.bigdecimal.Prime
-
return the smallest prime larger than n
- nextRandom8Bit() - Static method in class org.jmol.util.Shader
-
Implements RANDU algorithm for random noise in lighting/shading.
- nextReweightStep - Variable in class etomica.virial.MeterVirialBDBin
-
- nextReweightStep - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- nextReweightStep - Variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- nextReweightStep - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- nextRight - Variable in class etomica.util.TreeLinker
-
- nextSet() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
Returns the iterator's pair and unsets iterator.
- nextSetBit(int) - Method in class org.jmol.util.BitSet
-
Returns the index of the first bit that is set to true that occurs
on or after the specified starting index.
- nextVector() - Method in class etomica.config.ConformationChain
-
- nextVector() - Method in class etomica.config.ConformationChain2D
-
- nextVector() - Method in class etomica.config.ConformationChain3D
-
- nextVector() - Method in class etomica.config.ConformationChainZigZag
-
- nextVector() - Method in class etomica.config.ConformationChainZigZag2
-
- nf - Variable in class etomica.virial.ClusterChainSoft
-
- nf - Variable in class etomica.virial.ClusterSinglyConnected
-
- nf - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- nf - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- nf1 - Variable in class etomica.virial.ClusterChainHS
-
- nfBond - Variable in class etomica.virial.PYGenerator.IteratorEF
-
- nfctmx - Static variable in class etomica.potential.P2O2Bartolomei
-
- nFieldPoints - Variable in class etomica.graph.operations.Mul.MulParameters
-
- nGraft - Variable in class etomica.modules.colloid.ColloidGraphic.GraftAction
-
- nGraft - Variable in class etomica.modules.colloid.ColloidSim
-
- nGraft - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- Ni - Static variable in class etomica.meam.ParameterSetMEAM
-
- nIn - Static variable in class org.jmol.util.Shader
-
- nIndices - Variable in class etomica.virial.cluster.PermutationIterator
-
- nInner - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- nInsert - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- nInsert - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
-
- nInsert - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- nInsert - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
-
- nInsert - Variable in class etomica.models.oneDHardRods.MeterWidomMode
-
- nInsert - Variable in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- nInsert - Variable in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- Nitrogen - Class in etomica.chem.elements
-
Class for the Nitrogen element.
- Nitrogen(String) - Constructor for class etomica.chem.elements.Nitrogen
-
- Nitrogen(String, double) - Constructor for class etomica.chem.elements.Nitrogen
-
- nKs - Variable in class etomica.potential.EwaldSummation
-
- nLayer - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- nLayer - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- nLayer - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- nLayer - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- nLayer - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- nLayer - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- nLayer - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- nLayer - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- nLayer - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- nLeafAtoms - Variable in class etomica.atom.iterator.ANIntergroupCoupled
-
- nLeafAtoms - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- nlin - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- nlin3 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- nLookUp - Static variable in class etomica.space3d.Vector3D
-
- nLREP - Variable in class etomica.meam.PotentialCuLREP
-
- nm - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- nm - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- nm - Variable in class etomica.normalmode.HessianDB
-
- nm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- nm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- nm - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- nMax - Static variable in class etomica.veos.bigdecimal.PartitionsP
-
The maximum integer covered by the high end of the list.
- nMax - Static variable in class etomica.veos.bigdecimal.Prime
-
The maximum integer covered by the high end of the list.
- nMethane - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
-
- nMethane - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
-
- NModifier() - Constructor for class etomica.modules.crystalviewer.LatticeEditor.NModifier
-
- nMol - Variable in class etomica.normalmode.MeterSolidProps
-
- nMol - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- nMol - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- nMol - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- nMolecules - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule.Agent
-
- nMolecules - Variable in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- nMolecules - Variable in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- nMolecules - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- nMoments - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- nMoments - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- nMonoAcid - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- nMonoOl - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- nmrurlformat - Static variable in class org.jmol.script.Token
-
- nMu - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
-
- nMu - Variable in class etomica.normalmode.DataSourcePMu
-
- nNominalAtoms - Variable in class etomica.modules.droplet.DropletAtomic
-
- nO2 - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- nocontourlines - Static variable in class org.jmol.script.Token
-
- Node - Interface in etomica.graph.model
-
- node1ID - Variable in class etomica.graph.operations.MulFlexible.MulFlexibleParameters
-
- node2ID - Variable in class etomica.graph.operations.MulFlexible.MulFlexibleParameters
-
- NODE_NULL - Static variable in interface etomica.graph.traversal.Traversal
-
- nodeColor - Variable in class etomica.virial.cluster.VirialDiagrams
-
- nodeColor - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- nodeColor - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- nodeColors - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- nodeColors - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- nodeCount() - Method in interface etomica.graph.model.Graph
-
- nodeCount() - Method in class etomica.graph.model.impl.GraphImpl
-
- nodeId() - Method in class etomica.graph.operations.ConvParameters
-
- nodeId - Variable in class etomica.graph.operations.FactorOnce.FactorOnceParameters
-
- nodeId() - Method in class etomica.graph.operations.IntParameters
-
- NodeImpl - Class in etomica.graph.model.impl
-
- NodeImpl(byte, char, char) - Constructor for class etomica.graph.model.impl.NodeImpl
-
- NodePair - Class in etomica.graph.isomorphism
-
- NodePair(Byte, Byte) - Constructor for class etomica.graph.isomorphism.NodePair
-
- nodes() - Method in interface etomica.graph.model.Graph
-
- nodes() - Method in class etomica.graph.model.impl.GraphImpl
-
- nodesToString() - Method in interface etomica.graph.model.Graph
-
- nodesToString() - Method in class etomica.graph.model.impl.GraphImpl
-
- NodeVisitor - Interface in etomica.graph.model
-
- NoDoNotRemoveSpeciesButtonListener() - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval.NoDoNotRemoveSpeciesButtonListener
-
- nodots - Static variable in class org.jmol.script.Token
-
- nofill - Static variable in class org.jmol.script.Token
-
- noisyAdjustment - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
-
- nomesh - Static variable in class org.jmol.script.Token
-
- nominalBlockSize - Variable in class etomica.data.AccumulatorAverageCollapsing
-
- nominalBondL - Static variable in class etomica.virial.SpeciesAlkane
-
- nominalBondL - Static variable in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- nominalBondL - Static variable in class etomica.virial.SpeciesFactorySpheres2
-
- nominalBondTheta - Static variable in class etomica.virial.SpeciesAlkane
-
- nominalBondTheta - Static variable in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- nominalBondTheta - Static variable in class etomica.virial.SpeciesFactorySpheres2
-
- nominalBoxSize - Variable in class etomica.normalmode.MCMoveVolumeSolid
-
- nominalDiameter - Variable in class etomica.modules.droplet.EllipseDisplayAction
-
- nominalFluctuation - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- nominalFrequency - Variable in class etomica.integrator.mcmove.MCMove
-
Value giving nominal frequency for performing this move.
- nominalNumAtoms - Variable in class etomica.normalmode.DataSourcePN
-
- nominalScale - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- nominalTheta - Variable in class etomica.normalmode.MeterThetaDeviation
-
- nominalTimeStep - Variable in class etomica.graphics.DeviceDelaySlider
-
- nominalWeight - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- nominalWeight - Variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- nominalWeight - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- nonAdd - Variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- nonAdditive - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
-
- nonAdditive - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
-
- nonAdditive - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
-
- nonAdditive - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- nonAdditive - Variable in class etomica.virial.simulations.VirialH2OGCPMD.VirialParam
-
- nonAdditive - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- nonAdditive - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- nonAdditiveOnly - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
-
- nonAssociationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- nonAssociationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- nonAssociationPotential - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- NONE - Static variable in class etomica.virial.cluster.ClusterOperations
-
- none - Static variable in class org.jmol.script.Token
-
- nonLinearCG(FunctionMultiDimensionalDifferentiable, double[]) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- NonLinearConjugateGradients - Class in etomica.conjugategradient
-
- NonLinearConjugateGradients() - Constructor for class etomica.conjugategradient.NonLinearConjugateGradients
-
- NoOfSpheres - Variable in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- noOfSteps - Variable in class etomica.virial.GUI.models.ModelTemperatureAndSteps
-
- noReset - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
-
- norm - Variable in class etomica.math.Quaternion
-
- norm - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- norm - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- norm0 - Variable in class etomica.potential.P2SpheroPolyhedron
-
- norm1 - Variable in class etomica.potential.P2SpheroPolyhedron
-
- norm2 - Variable in class etomica.potential.P2SpheroPolyhedron
-
- normal - Variable in class etomica.dimer.SimDimerLJadatom
-
- normal - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- normalCount - Variable in class org.jmol.util.MeshSurface
-
- normalD - Variable in class etomica.dimer.IntegratorDimerMin
-
- normalDir - Variable in class etomica.dimer.SimDimerLJadatom
-
- normalize() - Method in class etomica.math.Quaternion
-
Normalizes the Quaternion q i.e.
- normalize() - Method in interface etomica.space.Vector
-
Normalizes this vector, so this.squared() == 1.
- normalize() - Method in class etomica.space1d.Vector1D
-
- normalize() - Method in class etomica.space2d.Vector2D
-
- normalize() - Method in class etomica.space3d.Vector3D
-
- normalize() - Method in class etomica.spaceNd.VectorND
-
- normalize() - Method in class etomica.veos.bigdecimal.BigSurd
-
Normalize to squarefree discriminant.
- normalize() - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Combine terms that can be written as a single surd.
- normalize() - Method in class etomica.veos.bigdecimal.Rational
-
Normalize to coprime numerator and denominator.
- normalize() - Method in class org.jmol.util.Vector3f
-
Normalizes this vector in place.
- normalizeG() - Method in class etomica.veos.bigdecimal.BigSurd
-
Normalize to coprime numerator and denominator in prefactor and discriminant
- NormalModeAnalysisDisplay1D - Class in etomica.normalmode
-
- NormalModeAnalysisDisplay1D(Space) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- NormalModeAnalysisDisplay1D.Applet - Class in etomica.normalmode
-
- NormalModeAnalysisDisplay1DGraphic - Class in etomica.normalmode
-
- NormalModeAnalysisDisplay1DGraphic(NormalModeAnalysisDisplay1D, Space) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- NormalModeAnalysisDisplay1DGraphic.Applet - Class in etomica.normalmode
-
- NormalModeAnalysisDisplay2D - Class in etomica.normalmode
-
Harmonic anaylsis for 2-D soft-sphere model
- NormalModeAnalysisDisplay2D(Space) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- NormalModeAnalysisDisplay2DGraphic - Class in etomica.normalmode
-
- NormalModeAnalysisDisplay2DGraphic(NormalModeAnalysisDisplay2D, Space) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- NormalModeAnalysisDisplay2DGraphic.Applet - Class in etomica.normalmode
-
- NormalModeAnalysisDisplay3D - Class in etomica.normalmode
-
- NormalModeAnalysisDisplay3D(Space) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- NormalModeAnalysisDisplay3D.Applet - Class in etomica.normalmode
-
- NormalModeAnalysisDisplay3DGraphic - Class in etomica.normalmode
-
Harmonic Oscillator 3D
- NormalModeAnalysisDisplay3DGraphic(NormalModeAnalysisDisplay3D, Space) - Constructor for class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- NormalModeAnalysisDisplay3DGraphic.Applet - Class in etomica.normalmode
-
- NormalModeEigenGetter - Class in etomica.normalmode
-
- NormalModeEigenGetter() - Constructor for class etomica.normalmode.NormalModeEigenGetter
-
- NormalModeEigenGetter - Class in etomica.paracetamol
-
- NormalModeEigenGetter() - Constructor for class etomica.paracetamol.NormalModeEigenGetter
-
- normalModes - Variable in class etomica.models.hexane.SimHarmonicHexane
-
- normalModes - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- normalModes - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- normalModes - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- normalModes - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- normalModes - Variable in class etomica.normalmode.MCMovePhaseAngle
-
- normalModes - Variable in class etomica.normalmode.MCMoveWV
-
- normalModes - Variable in class etomica.normalmode.MeterHarmonicEnergy
-
- normalModes - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- normalModes - Variable in class etomica.normalmode.MeterJacobian
-
- NormalModes - Interface in etomica.normalmode
-
Provides information about all the normal modes for a periodic system.
- normalModes - Variable in class etomica.normalmode.SimBennet
-
- normalModes - Variable in class etomica.normalmode.SimHarmonic
-
- normalModes - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- normalModes - Variable in class etomica.normalmode.SimModesJ
-
- normalModes - Variable in class etomica.normalmode.SimOverlap
-
- normalModes - Variable in class etomica.normalmode.SimOverlapLJ
-
- normalModes - Variable in class etomica.normalmode.SimOverlapLJModule
-
- normalModes - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- normalModes - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- normalModes - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- normalModes - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- normalModes - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- normalModes - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- normalModes - Variable in class etomica.normalmode.SimTargetUmbrella
-
- normalModes - Variable in class etomica.normalmode.SimUmbrella
-
- normalModes - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- NormalModes1DHR - Class in etomica.normalmode
-
Normal-mode quantities for a 1-dimensional system of hard rods.
- NormalModes1DHR(Boundary, int) - Constructor for class etomica.normalmode.NormalModes1DHR
-
- NormalModes2D - Class in etomica.normalmode
-
- NormalModes2D(Space, Boundary, Primitive, Basis) - Constructor for class etomica.normalmode.NormalModes2D
-
- NormalModes3D - Class in etomica.normalmode
-
- NormalModes3D(Space, Primitive, Basis) - Constructor for class etomica.normalmode.NormalModes3D
-
- NormalModesFromFile - Class in etomica.normalmode
-
Provides normal-mode information as obtained from a file read at
construction.
- NormalModesFromFile(String, int) - Constructor for class etomica.normalmode.NormalModesFromFile
-
- NormalModesMolecular - Class in etomica.normalmode
-
Uses analysis of 2nd derivatives to compute the normal modes for a Bravais lattice with a basis,
occupied by atoms that interact with a simple, spherically-symmetric soft potential.
- NormalModesMolecular(SpeciesWater4P, boolean, PotentialMaster, Box, int[], Primitive, int, LatticeSumMolecularCrystal.AtomicTensorAtomicPair, Space) - Constructor for class etomica.normalmode.NormalModesMolecular
-
- NormalModesPotential - Class in etomica.normalmode
-
Uses analysis of 2nd derivatives to compute the normal modes for a Bravais lattice with a basis,
occupied by atoms that interact with a simple, spherically-symmetric soft potential.
- NormalModesPotential(int[], Primitive, Basis, Potential2SoftSpherical, Space) - Constructor for class etomica.normalmode.NormalModesPotential
-
- NormalModesPotentialParacetamol - Class in etomica.paracetamol
-
Uses analysis of 2nd derivatives to compute the normal modes for a Bravais lattice with a basis,
occupied by atoms that interact with a simple, spherically-symmetric soft potential.
- NormalModesPotentialParacetamol(int[], Primitive, Basis, Space) - Constructor for class etomica.paracetamol.NormalModesPotentialParacetamol
-
- NormalModesPotentialParacetamol.Lattice2ndDerivative - Class in etomica.paracetamol
-
- NormalModesSoftSpherical - Class in etomica.normalmode
-
Computes the normal modes for a Bravais lattice occupied by atoms that interact
with a simple, spherically-symmetric soft potential, using analysis of second
derivatives.
- NormalModesSoftSpherical(int[], Primitive, Potential2SoftSpherical, Space) - Constructor for class etomica.normalmode.NormalModesSoftSpherical
-
- NormalModesVariable - Class in etomica.normalmode
-
- NormalModesVariable(Space, int, CoordinateDefinition) - Constructor for class etomica.normalmode.NormalModesVariable
-
- normals - Variable in class org.jmol.util.MeshSurface
-
- normalsTemp - Variable in class org.jmol.util.MeshSurface
-
- normalVector - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- normalWidth - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- Normix - Class in org.jmol.util
-
Provides quantization of normalized vectors so that shading for
lighting calculations can be handled by a simple index lookup
- Normix() - Constructor for class org.jmol.util.Normix
-
- NORMIX_NULL - Static variable in class org.jmol.util.Normix
-
- normixCount - Variable in class org.jmol.util.MeshSurface
-
- noRotScale - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- not() - Method in interface etomica.graph.model.Bitmap
-
Inverts the bits of this bitmap: bitmap = ~bitmap.
- not() - Method in class etomica.graph.model.impl.AbstractBitmap
-
- not() - Method in class etomica.graph.model.impl.BitmapOfLong
-
TIME = O(1).
- not() - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- NOT_ALLOWED - Static variable in enum etomica.units.Prefix
-
Constant used when invoking constructor of SimpleUnit class to indicate
that the unit does not permit the use of a prefix.
- NOTE_SCRIPT_FILE - Static variable in class org.jmol.viewer.JmolConstants
-
- notfrontonly - Static variable in class org.jmol.script.Token
-
- notifyEndOfRendering() - Method in interface org.jmol.api.ApiPlatform
-
- notifyEndOfRendering() - Method in class org.jmol.awt.Platform
-
- notifyEnergyChange(double) - Method in class etomica.integrator.IntegratorMC
-
Notifies the IntegratorMC that the energy changed allowing
the internal potential energy field to be updated.
- notifyNeedUpdate() - Method in class etomica.graphics.EtomicaPlot
-
Notify that the displayPlot has new data, but we're not showing.
- notifyNewMolecules(ISpecies, int, int) - Method in class etomica.box.Box
-
- notriangles - Static variable in class org.jmol.script.Token
-
- notzero - Variable in class etomica.virial.ClusterWheatleyHS
-
- notzero - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- nOut - Static variable in class org.jmol.util.Shader
-
- nOuter - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- NoValueOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.NoValueOptionHandler
-
- nOverlaps - Variable in class etomica.graphics.ColorSchemeOverlap
-
- nOverlaps - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- nPairs() - Method in class etomica.potential.Potential0Lrc
-
Returns the number of pairs formed from molecules of the current
species, in the given box.
- npairs - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- npairs - Variable in class etomica.virial.MeterVirialSWWE
-
- nPerm - Variable in class etomica.potential.P3HydrogenManzhos
-
- nPermutations - Variable in class etomica.virial.ClusterBonds
-
- nPermutations() - Method in class etomica.virial.ClusterBonds
-
Number of permutations of (and including) the basic cluster used when
calculating its value for a configuration
- nPoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
-
- nPoints - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
-
- nPoints - Variable in class etomica.virial.ClusterBonds
-
- nPoints - Variable in class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam
-
- nPoints - Variable in class etomica.virial.simulations.LJTSRefLJ.VirialLJParam
-
- nPoints - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
-
- nPoints - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialExternalFieldOverlapRho.VirialExternalFieldParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialGCPM.VirialGCPMParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialH2OGCPMD.VirialParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- nPoints - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialLJD.VirialLJParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
-
- nPoints - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- nPoints - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialSQWRecalcSmallMem.VirialHSParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialSW.VirialSWParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
-
- nPoints - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- npol - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- npowers - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- nPretendPoints - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- nPts - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- nPtsTabulated - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- nPtsTabulated - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- nPtsTabulated - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- nPtsTabulated - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- npun - Static variable in class etomica.potential.P2O2Bartolomei
-
- nRawData - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- nRawData - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- nRawDataDoubles - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- nRawDataDoubles - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- nrcMax - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
-
- nrcMax - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- nReactCO - Variable in class etomica.modules.catalysis.ReactionManagerCO
-
- nReacted - Variable in class etomica.modules.chainequilibrium.MeterConversion
-
- nRealPoints - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
-
- nRealShells - Variable in class etomica.potential.EwaldSummation
-
- nRejected - Variable in class etomica.integrator.IntegratorMD
-
- nRootField - Variable in class etomica.modules.clustergenerator.MyApplet
-
- nRows - Variable in class etomica.data.types.DataTable.DataInfoTable
-
- nRows - Variable in class etomica.data.types.DataTable.DataInfoTableFactory
-
- nRowsA - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- nSamples - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- nSamples - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- nSamples - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- nSamples - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- nSets - Variable in class org.jmol.util.MeshSurface
-
- nShapes - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- nShells - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- nShells - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- nShells - Variable in class etomica.meam.PotentialEAM_LS
-
- nShells - Variable in class etomica.potential.Potential2SoftSphericalLS
-
- nsite3 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- nsitea - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- nsiteb - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- nsitemax - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- nsites - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- nSlider - Variable in class etomica.modules.droplet.DropletGraphic
-
- nSlider - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- nSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- nSlider - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic.MySpeciesEditor
-
- nsp - Static variable in class etomica.potential.P2HydrogenPatkowski
-
- nsp - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- nSpheres - Variable in class etomica.virial.GUI.components.CollectionBondedPotentialAlkanes
-
- nSpheres - Variable in class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
-
- nSpheres - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- nSpheres - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- nSpheres1 - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
-
- nSpheres1 - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
-
- nSpheres1 - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
-
- nSpheres1 - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
-
- nSpheres2 - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
-
- nSpheres2 - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
-
- nSpheres2 - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
-
- nSpheres2 - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
-
- Nstar - Variable in class etomica.dimer.IntegratorDimerMin
-
- Nstar - Variable in class etomica.dimer.IntegratorDimerRT
-
- NstarDelta - Variable in class etomica.dimer.IntegratorDimerMin
-
- NstarDelta - Variable in class etomica.dimer.IntegratorDimerRT
-
- nStates - Variable in class etomica.tmmc.IntegratorTMMC
-
- nSubPoints - Variable in class etomica.math.numerical.AkimaSplineSmootherApp.PlotAction
-
- nSubPoints - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp.PlotAction
-
- nSurfaceBonds - Variable in class etomica.modules.catalysis.InteractionTracker.CatalysisAgent
-
- nSurfaceSites - Variable in class etomica.modules.catalysis.P2SquareWellBonding
-
- nSurfaceSites - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- nSurfactantSlider - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- nTag - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- nTag - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- nTag - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- nTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- nThreads - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- nThreads - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- nTimes - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- nTimes - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- nTimes - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- nTimes - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- ntpot - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- nTrial - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- nTrial - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- nTrial - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- nTrial - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- nTrials - Variable in class etomica.integrator.mcmove.MCMoveTracker
-
- nType - Variable in class etomica.models.nitrogen.SpeciesN2
-
- nType - Variable in class etomica.models.nitrogen.SpeciesN2B
-
- nType - Variable in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- nType - Variable in class etomica.paracetamol.SpeciesParacetamol
-
- ntypemax - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- nTypes - Variable in class etomica.virial.ClusterWheatleySoftBDMix
-
- nTypes - Variable in class etomica.virial.ClusterWheatleySoftMix
-
- nTypes - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
-
- nTypes - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
-
- nTypes - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- nucleic - Static variable in class org.jmol.script.Token
-
- nufac0 - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- Null - Class in etomica.units.dimensions
-
Dimension specified dimensionless quantities which have no other interpretation
(e.g., the quantity is not known to be an angle, or a fraction).
- NULL_NODE - Static variable in interface etomica.graph.isomorphism.SearchState
-
- nullCollisionTime - Variable in class etomica.integrator.IntegratorHard.Agent
-
- nullPair() - Static method in class etomica.graph.isomorphism.NodePair
-
- nullPotential - Variable in class etomica.integrator.IntegratorHard.Agent
-
- nullPotentialManager - Variable in class etomica.integrator.IntegratorHard
-
- nullRegionMethod - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
-
- nullRegionMethod - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- nullRegionMethod - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- num - Variable in class etomica.virial.ClusterICPYC
-
- numActions - Variable in class etomica.action.activity.ActivityGroupParallel
-
- numActions - Variable in class etomica.action.activity.ActivityGroupSeries
-
- numAlpha - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- numAlpha - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- numAlpha - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- numAlpha - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- numAlpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
-
- numAlpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- numAlpha - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- numAlpha - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- numAlpha - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- numAlpha - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- numAlpha - Variable in class etomica.normalmode.MeterTargetTP
-
- numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
-
- numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- numAlpha - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- numAlpha - Variable in class etomica.overlap.MeterOverlap
-
- numAlpha - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- numAlpha - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- numAssociatedAtoms - Variable in class etomica.association.MCMoveVolumeAssociated
-
- numAssociatedMolecules - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- numAtoms - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
-
- numAtoms - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- numAtoms - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- numAtoms - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- numAtoms - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
-
- numAtoms - Variable in class etomica.chem.models.ModelChain
-
- numAtoms - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- numAtoms - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
-
- numAtoms - Variable in class etomica.freeenergy.npath.SimLattice.LjMC3DParams
-
- numAtoms - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
-
- numAtoms - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
-
- numAtoms - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
-
- numAtoms - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- numAtoms - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
-
- numAtoms - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- numAtoms - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- numAtoms - Variable in class etomica.mappedRdf.MappedRdf.LJMDParams
-
- numAtoms - Variable in class etomica.mappedvirial.MappedU.LJMDParams
-
- numAtoms - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
-
- numAtoms - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
-
- numatoms - Variable in class etomica.meam.EFSTungsten.Params
-
- numAtoms - Variable in class etomica.metastable.LJmuVT.LJMCParams
-
- numAtoms - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- numAtoms - Variable in class etomica.metastable.LJNVT.LJMCParams
-
- numAtoms - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- numAtoms - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- numAtoms - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- numAtoms - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- numAtoms - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- numAtoms - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- numAtoms - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- numAtoms - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- numAtoms - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- numAtoms - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- numAtoms - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- numAtoms - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
-
- numAtoms - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- numAtoms - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
-
- numAtoms - Variable in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
-
- numAtoms - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
-
- numAtoms - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
-
- numAtoms - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- numAtoms - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
-
- numAtoms - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- numAtoms - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- numAtoms - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- numAtoms - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- numAtoms - Variable in class etomica.surfacetension.LJMC.LJMCParams
-
- numAtoms - Variable in class etomica.tests.TestHSMD3D.SimParams
-
- numAtoms - Variable in class etomica.tests.TestLJGCMC3D.SimParams
-
- numAtoms - Variable in class etomica.tests.TestLJMC3D.SimParams
-
- numAtoms - Variable in class etomica.tests.TestSWChain.SimParams
-
- numAtoms - Variable in class etomica.virial.CoordinatePairLeafSet
-
- numAtoms - Variable in class etomica.virial.CoordinatePairMoleculeSet
-
- numAtoms - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- numAtomsLattice - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- numAtomsMove - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- numBeads - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- numberFraction - Variable in class etomica.species.SpeciesSpheresHetero
-
- numberMolecules - Variable in class etomica.AlkaneEH.CH4NVT.Param
-
- numberMolecules - Variable in class etomica.AlkaneEH.DHS_NVT.Param
-
- numberMolecules - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- numberMolecules(ISpecies, int) - Method in class etomica.box.BoxEventManager
-
- numberMolecules - Variable in class etomica.dielectric.DHS_NVT.Param
-
- numberMolecules - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- numberMolecules - Variable in class etomica.dielectric.TIP4P_NVT.Param
-
- numberOfStates(Box) - Method in interface etomica.tmmc.MacrostateManager
-
Number of expected macrostates in the box.
- NumbersToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.NumbersToggler
-
- numCarbons - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- numCarbons - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- numCarbons - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- numCells - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- numCells - Variable in class etomica.nbr.cell.NeighborCellManager
-
- numCellsSlider - Variable in class etomica.modules.sam.SamGraphic
-
- numCH2 - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- numCH2 - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- numCollapseBins - Variable in class etomica.data.history.HistoryCollapsing
-
- numDelete - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- numDeleteCandidateNbrs - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- numDeleteCandidateNbrs - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- numDiagram - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
-
- numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
-
- numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
-
- numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
-
- numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
-
- numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
-
- numDiagram - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
-
- numDiagrams() - Method in class etomica.virial.ClusterChainHS
-
- numDiagrams() - Method in class etomica.virial.ClusterChainSoft
-
- numDiagrams() - Method in class etomica.virial.ClusterSinglyConnected
-
- numEquilibrationSubsteps - Variable in class etomica.thermointegration.IntegratorThermodynamic
-
- numer() - Method in class etomica.veos.bigdecimal.Rational
-
Get the numerator.
- numerator - Variable in class etomica.math.Rational
-
- numerator() - Method in class etomica.math.Rational
-
Returns the numerator.
- NumericalDerivativeEnergyParacetamol - Class in etomica.paracetamol
-
- NumericalDerivativeEnergyParacetamol(Box, PotentialMaster) - Constructor for class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
-
- NumericFeature - Class in etomica.compatibility
-
- NumericFeature(String, double) - Constructor for class etomica.compatibility.NumericFeature
-
- numEval - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- numExtraTargetClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- NumFieldNodes - Class in etomica.graph.property
-
Simple class that returns the number of field nodes.
- NumFieldNodes() - Constructor for class etomica.graph.property.NumFieldNodes
-
- numH - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- numH - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- numIncomingValues - Variable in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- numInnerSteps - Variable in class etomica.freeenergy.npath.IntegratorImageMultistepMD
-
- numInnerSteps - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- numInsert - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- numInserts - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- numMembraneLayers - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- numMembraneLayers - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- numMer - Variable in class etomica.association.MCMoveVolumeAssociated
-
- numMer - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- numMol - Variable in class etomica.models.nitrogen.MeterOrientationOrderParameter
-
- numMolec - Variable in class etomica.models.nitrogen.MCMoveVolumeN2
-
- numMolec - Variable in class etomica.models.nitrogen.P0LatticeEnergyCorrec
-
- numMolecule - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- numMolecule - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- numMolecule - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- numMolecule - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- numMolecule - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- numMolecules - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
-
- numMolecules - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- numMolecules - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
-
- numMolecules - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- numMolecules - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- numMolecules - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- numMolecules - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- numMolecules - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.MinimizeHCP
-
- numMolecules - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimBennet.SimBennetParam
-
- numMolecules - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
-
- numMolecules - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
-
- numMolecules - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
-
- numMolecules - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
-
- numMolecules - Variable in class etomica.potential.EwaldSumMolecules
-
- numMolecules - Variable in class etomica.simulation.BenchSimSWChain
-
- numMolecules - Variable in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol.VirialParam
-
- numMolecules - Variable in class etomica.virial.simulations.SimulationVirial
-
- numMolecules - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
-
- numMolecules - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- numMolecules - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- numMolecules - Variable in class etomica.virial.simulations.VirialLJBridge.VirialLJParam
-
- numMolecules - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
-
- numMolecules - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
-
- numMolecules - Variable in class etomica.virial.simulations.VirialRowleyAlcohol.VirialParam
-
- numMolecules - Variable in class etomica.virial.simulations.VirialTraPPEAlcohol.VirialParam
-
- numMolecules0 - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- numNeighborCandidatesOnDelete - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- numNeighborCandidatesOnDelete - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- numNeighbors - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- numNeighbors - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- numNewDeleteCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- numNewDeleteCandidates - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- numNonAdditiveNeeded - Variable in class etomica.virial.ClusterSumMultibody
-
- numP - Variable in class etomica.normalmode.MeterDDP
-
- numP - Variable in class etomica.normalmode.MeterDP
-
- numP - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- NumRootNodes - Class in etomica.graph.property
-
Simple class that returns the number of root nodes.
- NumRootNodes() - Constructor for class etomica.graph.property.NumRootNodes
-
- numRuns - Variable in class etomica.metastable.LJmuVT.LJMCParams
-
- numRuns - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- numRuns - Variable in class etomica.metastable.LJNVT.LJMCParams
-
- numSteps - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
-
- numSteps - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
-
- numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
-
- numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
-
- numSteps - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
-
- numSteps - Variable in class etomica.mappedRdf.MappedRdf.LJMDParams
-
- numSteps - Variable in class etomica.mappedvirial.MappedU.LJMDParams
-
- numSteps - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
-
- numSteps - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
-
- numsteps - Variable in class etomica.meam.EFSTungsten.Params
-
- numSteps - Variable in class etomica.metastable.LJmuVT.LJMCParams
-
- numSteps - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- numSteps - Variable in class etomica.metastable.LJNVT.LJMCParams
-
- numSteps - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
-
- numSteps - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- numSteps - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
-
- numSteps - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- numSteps - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- numSteps - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- numSteps - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- numSteps - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- numSteps - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
-
- numSteps - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
-
- numSteps - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
-
- numSteps - Variable in class etomica.normalmode.SimBennet.SimBennetParam
-
- numSteps - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
-
- numSteps - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
-
- numSteps - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
-
- numSteps - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
-
- numSteps - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
-
- numSteps - Variable in class etomica.simulation.BenchSimSWChain
-
- numSteps - Variable in class etomica.tests.TestHSMD3D.SimParams
-
- numSteps - Variable in class etomica.tests.TestLJGCMC3D.SimParams
-
- numSteps - Variable in class etomica.tests.TestLJMC3D.SimParams
-
- numSteps - Variable in class etomica.tests.TestSWChain.SimParams
-
- numSteps - Variable in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
-
- numSteps - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialAceticAcid.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialB3C1TIP4Pwater.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialB3C2TIP4Pwater.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialExternalFieldOverlapRho.VirialExternalFieldParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialGCPM.VirialGCPMParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialH2OGCPMD.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialLJBridge.VirialLJParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialLJD.VirialLJParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
-
- numSteps - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialRowleyAlcohol.VirialParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialSW.VirialSWParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- numSteps - Variable in class etomica.virial.simulations.VirialTraPPEAlcohol.VirialParam
-
- numSubSteps - Variable in class etomica.overlap.IntegratorOverlap
-
- numSubsteps - Variable in class etomica.thermointegration.IntegratorThermodynamic
-
- numSum - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- numSum - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- numSum - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
-
- numSum - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- numSum - Variable in class etomica.normalmode.MeterWorkTargetBennet
-
- numSum - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- numSum - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- numSum - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- numtm - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- numTrial - Variable in class etomica.models.hexane.MCMoveCBMC
-
- numTrials - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- numUnsafe - Variable in class etomica.nbr.list.NeighborListManager
-
- numUpdates - Variable in class etomica.nbr.list.NeighborListManager
-
- numV - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
-
- numV - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- numWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- numXCells - Variable in class etomica.modules.sam.Sam
-
- numZCells - Variable in class etomica.modules.sam.Sam
-
- nValue(Token) - Static method in class org.jmol.script.ScriptVariable
-
- nve - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- nvt - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
-
- nx - Variable in class etomica.normalmode.MeterPlaneSlip
-
- ny - Variable in class etomica.normalmode.MeterPlaneSlip
-
O
- obj - Variable in class etomica.util.TreeLinker
-
- object - Variable in class etomica.graphics.DataTagBag
-
- object - Variable in class etomica.modifier.ModifierGeneral
-
- ObjectWrapper<T> - Class in etomica.meta.wrappers
-
- ObjectWrapper(T, SimulationModel, boolean) - Constructor for class etomica.meta.wrappers.ObjectWrapper
-
- objectWriter() - Static method in class etomica.server.EtomicaServer
-
- occupancy - Static variable in class org.jmol.script.Token
-
- occupants() - Method in class etomica.nbr.cell.Cell
-
- occupants() - Method in class etomica.nbr.cell.molecule.CellMolecular
-
- Oelement - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- of(double...) - Static method in interface etomica.space.Vector
-
Returns a Vector initialized to the given set of values.
- of(int...) - Static method in interface etomica.space.Vector
-
Returns a Vector initialized to the given set of values (cast to double).
- off - Static variable in class org.jmol.script.Token
-
- officialRelease - Static variable in class org.jmol.viewer.JmolConstants
-
- offScreen - Variable in class etomica.graphics.DisplayCanvas
-
- offset - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
-
- offset - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- offset - Variable in class etomica.modules.sam.P1Sinusoidal
-
- offset - Variable in class etomica.normalmode.SimOverlapLJModule.MeterPotentialEnergyDifference
-
- offset - Variable in class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
-
- offset - Variable in class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
-
- offset - Variable in class org.jmol.util.MeshSurface
-
- offset0 - Variable in class etomica.normalmode.MeterPlaneSlip
-
- offsetDim - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- offsetDim - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
-
- offsetDim - Variable in class etomica.freeenergy.npath.SimLattice.LjMC3DParams
-
- offsetDim - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
-
- old - Variable in class etomica.virial.ClusterChainHS
-
- oldB - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- oldB - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- oldBondlengths - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- oldBoxSize - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- oldCenter - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- oldCenter - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- oldColors - Variable in class etomica.association.ColorSchemeSmer
-
- oldDiagram - Variable in class etomica.virial.ClusterSumStickyEF
-
- oldDirtyAtom - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- oldDirtyAtom - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- oldDirtyAtom - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- oldDirtyAtom - Variable in class etomica.virial.ClusterTree
-
- oldEigenVectors - Variable in class etomica.normalmode.MCMoveWV
-
- oldEnergy - Variable in class etomica.integrator.IntegratorMD
-
- oldEpsilon - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
-
- oldG - Variable in class etomica.modules.droplet.EllipseDisplayAction
-
- oldGeo - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- oldGraphs - Static variable in class etomica.graph.isomorphism.Match
-
- oldLnA - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- oldLnA - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- oldMu - Variable in class etomica.models.co2.PNCO2GCPM
-
- oldMu - Variable in class etomica.models.co2.PNGCPM
-
- oldOrientations - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- oldPartners - Variable in class etomica.potential.PotentialReactive.BondChangeData
-
- oldPhaseAngles - Variable in class etomica.normalmode.MCMovePhaseAngle
-
- oldPosition - Variable in class etomica.integrator.mcmove.MCMoveAtomInRegion
-
- oldPosition - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- oldPosition - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- oldPositionAgentManager - Variable in class etomica.integrator.IntegratorMD
-
- oldPositions - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- oldPositions - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- oldPositions - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- oldPositions - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- oldPositions - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- oldPotentialEnergy - Variable in class etomica.integrator.IntegratorMD
-
- oldQ - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
-
- oldR - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
-
- oldSigma - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
-
- oldStep - Variable in class etomica.modules.rosmosis.MeterFlux
-
- oldTime - Variable in class etomica.modules.rosmosis.MeterFlux
-
- oldTotalCosTheta - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- oldValue - Variable in class etomica.modules.adsorption.ModifierPMu
-
- oldValue - Variable in class etomica.virial.simulations.ModifierTPI
-
- oldWaveVectors - Variable in class etomica.normalmode.MCMoveWV
-
- OLIVE - Static variable in class org.jmol.util.Colix
-
- omdth - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- omega() - Method in class etomica.veos.bigdecimal.Ifactor
-
The sum of the prime factor exponents, without multiplicity.
- omega - Static variable in class org.jmol.script.Token
-
- omega2 - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- omega2Table - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- omega2Table - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- omegaSquared - Variable in class etomica.normalmode.MeterHarmonicEnergy
-
- omegaSquared - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- omegaTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- omegaTolerance - Variable in class etomica.integrator.IntegratorRigidIterative
-
- omegaTolerance - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- ON - Static variable in class etomica.util.Debug
-
true if any debugging should be done
- on - Static variable in class org.jmol.script.Token
-
- onClose(Session) - Method in class etomica.server.resources.ConfigurationWebsocket
-
- onClose(Session) - Method in class etomica.server.resources.data.DataStreamWebsocket
-
- ONE - Static variable in class etomica.graph.model.BitmapFactory
-
- ONE - Static variable in class etomica.veos.bigdecimal.BigSurd
-
The value of one.
- ONE - Static variable in class etomica.veos.bigdecimal.BigSurdVec
-
The value of one.
- ONE - Static variable in class etomica.veos.bigdecimal.Ifactor
-
- oneEVal - Variable in class etomica.normalmode.IntegratorHarmonic
-
- oneIterate - Variable in class etomica.molecule.iterator.MoleculeIteratorAll
-
- oneOverSqrtOmega2 - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- oneOverSqrtOmega2 - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- onError(Session, Throwable) - Method in class etomica.server.resources.ConfigurationWebsocket
-
- onError(Session, Throwable) - Method in class etomica.server.resources.data.DataStreamWebsocket
-
- ones - Static variable in class etomica.data.types.DataDoubleBDArray
-
- oneWV - Variable in class etomica.normalmode.IntegratorHarmonic
-
- onlyDoublyConnectedCB - Variable in class etomica.modules.clustergenerator.MyApplet
-
- onlyRootPt - Variable in class etomica.graph.operations.MulFlexible.MulFlexibleParameters
-
- onlySinglyConnectedCB - Variable in class etomica.modules.clustergenerator.MyApplet
-
- onlyUnique - Variable in class etomica.graph.operations.AllIsomorphs.AllIsomorphsParameters
-
- onMessage(Session, String) - Method in class etomica.server.resources.EchoServer
-
- onOpen(Session, String) - Method in class etomica.server.resources.ConfigurationWebsocket
-
- onOpen(Session, String, String) - Method in class etomica.server.resources.data.DataStreamWebsocket
-
- onOpen(Session) - Method in class etomica.server.resources.EchoServer
-
- onSourceTranscodingSuccess(SVGConverterSource, File) - Method in class etomica.graph.view.rasterizer.DefaultSVGConverterController
-
Invoked when the rasterizer successfully transcoded
the input source.
- onSourceTranscodingSuccess(SVGConverterSource, File) - Method in class etomica.graph.view.rasterizer.Main
-
- onSourceTranscodingSuccess(SVGConverterSource, File) - Method in interface etomica.graph.view.rasterizer.SVGConverterController
-
Invoked when the rasterizer successfully transcoded
the input source.
- onSwitch - Variable in class etomica.models.nitrogen.PRotConstraint
-
- OO1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- OO1 - Variable in class etomica.association.BiasVolumeAceticAcid
-
- OO2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- OO2 - Variable in class etomica.association.BiasVolumeAceticAcid
-
- oops - Variable in class etomica.models.co2.PNCO2GCPM
-
- oops - Variable in class etomica.models.co2.PNGCPM
-
- op - Variable in class etomica.graph.operations.UnaryChain
-
- OPAQUE_MASK - Static variable in class org.jmol.util.Colix
-
- open() - Method in interface etomica.graph.engine.Viewer
-
- open() - Method in class etomica.graph.viewer.ClusterViewer
-
- openAlkaneView() - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- openFile() - Method in class etomica.zeolite.MSDCoordWriter
-
- openFW(String) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
Writes collected overlap data (for the "middle" alpha) to a file.
- openFW(String) - Method in class etomica.normalmode.MeterTargetTP
-
Writes collected overlap data (for the "middle" alpha) to a file.
- openSimEnvParamView() - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- openStream() - Method in class etomica.graph.view.rasterizer.SVGConverterDocumentSource
-
- openStream() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
-
- openStream() - Method in interface etomica.graph.view.rasterizer.SVGConverterSource
-
Gets a TranscoderInput for that source
- openStream() - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
-
- opEQ - Static variable in class org.jmol.script.Token
-
- optimizeHigherbVirial(int, int, double, double) - Method in class etomica.math.numerical.VirialOptimizer
-
- optimizeRvdwWMin(P2QChemInterpolated) - Method in class etomica.potential.P2QChemInterpolated
-
- optimizeRvdwWuTT3757(P2QChemInterpolated) - Method in class etomica.potential.P2QChemInterpolated
-
- optionMap - Static variable in class etomica.graph.view.rasterizer.Main
-
Static map containing all the option handlers able to analyze the
various options.
- Options() - Constructor for class etomica.parser.ParserLAMMPS.Options
-
- opToggle - Static variable in class org.jmol.script.Token
-
- or(Bitmap) - Method in interface etomica.graph.model.Bitmap
-
Updates this bitmap with the result of the bitwise AND with the other bitmap: bitmap
= (bitmap | other).
- or(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- or(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong
-
TIME = O(1) for a compatible instance.
- or(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- or(BitSet) - Method in class org.jmol.util.BitSet
-
Performs a logical OR of this bit set with the bit set argument.
- or01 - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- or01 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- or01 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- or02 - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- or02 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- or02 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- or11 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- or11 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- or12 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- or12 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- or2 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- or3 - Variable in class etomica.potential.P3Induction
-
- ORANGE - Static variable in class org.jmol.util.Colix
-
- order - Variable in class etomica.virial.MayerPTAtt
-
- order - Variable in class etomica.virial.MayerSphericalPTAtt
-
- order - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
-
- orderBeta - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- org.jmol.api - package org.jmol.api
-
- org.jmol.awt - package org.jmol.awt
-
- org.jmol.constant - package org.jmol.constant
-
- org.jmol.g3d - package org.jmol.g3d
-
- org.jmol.script - package org.jmol.script
-
- org.jmol.util - package org.jmol.util
-
- org.jmol.viewer - package org.jmol.viewer
-
- orH2O3 - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- orientation - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- orientation - Variable in class etomica.molecule.MoleculeOriented
-
- orientation - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- orientation - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- Orientation1D - Class in etomica.space1d
-
Orientation in a 1-dimensional space.
- Orientation1D() - Constructor for class etomica.space1d.Orientation1D
-
Construct with default orientation of +1.
- Orientation2D - Class in etomica.space2d
-
Orientation in a 2-dimensional space.
- Orientation2D() - Constructor for class etomica.space2d.Orientation2D
-
Default constructor sets orientation angle to zero.
- Orientation2D(Vector) - Constructor for class etomica.space2d.Orientation2D
-
Constructs with orientation as specified by the given angle theta.
- Orientation3D - Class in etomica.space3d
-
- Orientation3D(Space) - Constructor for class etomica.space3d.Orientation3D
-
Default constructor sets orientation to point in the X direction.
- OrientationAgentSource() - Constructor for class etomica.models.nitrogen.CoordinateDefinitionNitrogen.OrientationAgentSource
-
- OrientationAgentSource() - Constructor for class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource
-
- OrientationAgentSource() - Constructor for class etomica.paracetamol.CoordinateDefinitionParacetamol.OrientationAgentSource
-
- OrientationCalc - Interface in etomica.molecule
-
Interface for a class that can calculate the orientation of a molecule or
to set the orientation of a molecule.
- OrientationCalcAtom - Class in etomica.molecule
-
OrientationCalc implementation that handles a monotomic oriented molecule.
- OrientationCalcAtom() - Constructor for class etomica.molecule.OrientationCalcAtom
-
- OrientationCalcQuaternion - Interface in etomica.molecule
-
OrientationCalc interface that handles quaternions (as a a double array)
instead of an Orientation object.
- OrientationCalcWater3P - Class in etomica.models.water
-
- OrientationCalcWater3P(Space) - Constructor for class etomica.models.water.OrientationCalcWater3P
-
- OrientationCalcWater4P - Class in etomica.models.water
-
- OrientationCalcWater4P(Space) - Constructor for class etomica.models.water.OrientationCalcWater4P
-
- OrientationFull3D - Class in etomica.space3d
-
- OrientationFull3D(Space) - Constructor for class etomica.space3d.OrientationFull3D
-
Default constructor sets orientation to point in the X direction.
- orientationManager - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- orientationManager - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- orientationManager - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- orientationPlot - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- orientationProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- orientationProfilePump - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- orientationSelector - Variable in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- orientationX - Variable in class etomica.normalmode.ConformationHSDimer
-
- OrientedAgentSource() - Constructor for class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedAgentSource
-
- OrientedFullSite(Vector, Color, double) - Constructor for class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedFullSite
-
- OrientedSite(double, Color, double) - Constructor for class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedSite
-
- orientVector - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- originalGageLength - Variable in class etomica.modules.materialfracture.MeterElongation
-
- originalGageLength - Variable in class etomica.modules.materialfracture.MeterStrain
-
- originalPosition - Variable in class etomica.data.meter.MeterRMSD
-
- origins - Variable in class etomica.space.BoundaryRectangularNonperiodic
-
- OrnsteinZernike - Class in etomica.virial
-
- OrnsteinZernike() - Constructor for class etomica.virial.OrnsteinZernike
-
- ortho - Variable in class etomica.dimer.IntegratorDimerRT
-
- ortho2 - Variable in class etomica.dimer.IntegratorDimerRT
-
- OrthogonalPolynomial - Class in etomica.densityofstate
-
- OrthogonalPolynomial() - Constructor for class etomica.densityofstate.OrthogonalPolynomial
-
- osg - Variable in class etomica.graphics.DisplayCanvas
-
- osg - Variable in class etomica.modules.clustergenerator.Plot
-
- osg - Variable in class etomica.util.Grabber.ImagePanel
-
- Osmosis - Class in etomica.modules.osmosis
-
Osmosis module.
- Osmosis(OsmosisSim, Space) - Constructor for class etomica.modules.osmosis.Osmosis
-
- Osmosis.Applet - Class in etomica.modules.osmosis
-
- Osmosis.InitializeMolecules - Class in etomica.modules.osmosis
-
- Osmosis.MyWall - Class in etomica.modules.osmosis
-
- osmosisPMeter - Variable in class etomica.modules.osmosis.Osmosis
-
- OsmosisSim - Class in etomica.modules.osmosis
-
Osmosis simulation.
- OsmosisSim(Space) - Constructor for class etomica.modules.osmosis.OsmosisSim
-
- otherAngles - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- otherAngles - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- otherAngles - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- otherDensities - Variable in class etomica.normalmode.MeterDDP
-
- otherDensities - Variable in class etomica.normalmode.MeterDP
-
- otherFrac - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- otherFrac - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- otherPotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- otherPurePotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
-
- otherPurePotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- otherPurePotentials - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
-
- otherRho - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- otherSpecies - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- otherTemperature - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- otherTemperatures - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- otherTemperatures - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- otherTemperatures - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- otherTemperatures - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- otherTemperatures - Variable in class etomica.normalmode.MeterTargetTP
-
- otherTemperatures - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- otherTemperatures - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- otherTemperatures - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- oType - Variable in class etomica.models.rowley.SpeciesEthanol
-
- oType - Variable in class etomica.models.rowley.SpeciesMethanol
-
- oType - Variable in class etomica.models.traPPE.SpeciesMethanol
-
- oType - Variable in class etomica.models.water.SpeciesWater3P
-
- oType - Variable in class etomica.models.water.SpeciesWater3POriented
-
- oType - Variable in class etomica.models.water.SpeciesWater4P
-
- oType - Variable in class etomica.models.water.SpeciesWater4PCOM
-
- oType - Variable in class etomica.models.water.SpeciesWater4POriented
-
- oType - Variable in class etomica.paracetamol.SpeciesParacetamol
-
- oType - Variable in class etomica.virial.SpeciesTraPPECO2
-
- out - Variable in class etomica.metastable.LJmuVT.LJMCParams
-
- out - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- out - Variable in class etomica.metastable.LJNVT.LJMCParams
-
- outData - Variable in class etomica.data.DataDistributer
-
- outData - Variable in class etomica.data.DataGroupSplitter
-
- outData - Variable in class etomica.data.DataSplitter
-
- outDegree - Variable in class etomica.virial.ClusterSumHS
-
- outDegree - Variable in class etomica.virial.ClusterWheatleyHS
-
- outDegree - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- outDegreeCore - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- outDegreeWell - Variable in class etomica.virial.ClusterWheatleyExtendSW
-
- outNData - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- outNDataInfo - Variable in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- output - Variable in class etomica.modules.clustergenerator.MyApplet
-
- outputArea - Variable in class etomica.util.Grabber
-
- outputfilename - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- outputname - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- outputname - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- outputname - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- outputname - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- outputname - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- outputname - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- outputname - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- outputname - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
-
- outRadius - Variable in class etomica.atom.AtomTypeSpheroPolyhedron
-
- oValue(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- OverflowShift - Class in etomica.graphics
-
- overlapAvgA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- overlapAvgB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- overlapBlockCovSum - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- overlapCorrelationSum - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- overlapFirstBlock - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- overlapMostRecentBlock - Variable in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- Oxygen - Class in etomica.chem.elements
-
Class for the Oxygen element.
- Oxygen(String) - Constructor for class etomica.chem.elements.Oxygen
-
- Oxygen(String, double) - Constructor for class etomica.chem.elements.Oxygen
-
- oy - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
P
- P - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- P - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- P - Variable in class etomica.atom.iterator.ApiIntergroupExchange
-
- p - Variable in class etomica.box.RandomPositionSourceDeformable
-
- p - Variable in class etomica.box.RandomPositionSourceRectangular
-
- p - Variable in class etomica.normalmode.MeterDDP
-
- p - Variable in class etomica.normalmode.MeterDP
-
- p - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- P - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- P - Variable in class etomica.potential.P2HePCKLJS
-
- p - Variable in class etomica.potential.P2HydrogenPatkowski
-
- p - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- p - Variable in class etomica.potential.PotentialAtomicSum
-
- p - Variable in class etomica.potential.PotentialMolecularSum
-
- p - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- p - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- p - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- p - Variable in class etomica.virial.cluster.VirialDiagrams
-
- p - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- p - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- p - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- p - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- p - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- P - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- p - Variable in class etomica.virial.PotentialNonAdditive
-
- p0 - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- P0LatticeEnergyCorrec - Class in etomica.models.nitrogen
-
The lattice energy correction for Nitrogen model
zero-body interaction
All the parameters are determined from the fitted equation.
- P0LatticeEnergyCorrec(Space) - Constructor for class etomica.models.nitrogen.P0LatticeEnergyCorrec
-
- P0Lrc(Space, Potential2Soft, Potential2Soft, AtomType[]) - Constructor for class etomica.potential.P2SoftSphericalTruncated.P0Lrc
-
- P0ReactionField(Space, P2ReactionFieldDipoleTruncated) - Constructor for class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- p1 - Variable in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- p1 - Variable in class etomica.freeenergy.npath.IntegratorImageMultistepMD
-
- p1 - Variable in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- p1 - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- p1 - Variable in class etomica.freeenergy.npath.MCMoveAtomNPath
-
- p1 - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- p1 - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- p1 - Variable in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
-
- p1 - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- p1 - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- p1 - Variable in class etomica.normalmode.MeterDDP
-
- p1 - Variable in class etomica.normalmode.MeterDP
-
- p1 - Variable in class etomica.normalmode.MeterTargetTP
-
- p1 - Variable in class etomica.potential.P2HydrogenPatkowski
-
- p1 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- p1 - Variable in class etomica.virial.ClusterExchange
-
- p1 - Variable in class etomica.virial.P1IntraLambda
-
- p1BoundaryA - Variable in class etomica.modules.mu.Mu
-
- p1BoundaryB - Variable in class etomica.modules.mu.Mu
-
- p1Constraint - Variable in class etomica.normalmode.HTTPSoftSphereSim
-
- P1Constraint - Class in etomica.normalmode
-
- P1Constraint(Space, double, Box, CoordinateDefinition) - Constructor for class etomica.normalmode.P1Constraint
-
- p1Constraint - Variable in class etomica.normalmode.SimCalcSLJ
-
- p1Constraint - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- p1Constraint - Variable in class etomica.normalmode.SimOverlapLJ
-
- p1Constraint - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- p1Constraint - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- P1ConstraintNbr - Class in etomica.normalmode
-
- P1ConstraintNbr(Space, double) - Constructor for class etomica.normalmode.P1ConstraintNbr
-
- P1ConstraintNbr(Space, double, double) - Constructor for class etomica.normalmode.P1ConstraintNbr
-
- P1ConstraintNbrHcp - Class in etomica.normalmode
-
- P1ConstraintNbrHcp(Space, double, Box) - Constructor for class etomica.normalmode.P1ConstraintNbrHcp
-
- p1Counter - Variable in class etomica.normalmode.P1ConstraintNbrHcp
-
- P1ExternalField - Class in etomica.potential
-
- P1ExternalField(Space) - Constructor for class etomica.potential.P1ExternalField
-
- P1HardBoundary - Class in etomica.potential
-
Potential that places hard repulsive walls coinciding with the
boundary of the box, which is assumed to be rectangular in shape.
- P1HardBoundary(Space) - Constructor for class etomica.potential.P1HardBoundary
-
- P1HardBoundary(Space, boolean) - Constructor for class etomica.potential.P1HardBoundary
-
- P1HardMovingBoundary - Class in etomica.potential
-
Potential that places hard repulsive walls that move and
accelerate subject to an external force field (pressure).
- P1HardMovingBoundary(Space, Boundary, int, double, boolean) - Constructor for class etomica.potential.P1HardMovingBoundary
-
Constructor for a hard moving (and accelerating) boundary.
- P1HardPeriodic - Class in etomica.potential
-
pseudo-potential for a "collision" time to update colliders for periodic boundaries
- P1HardPeriodic(Space) - Constructor for class etomica.potential.P1HardPeriodic
-
Returns an instance of P1HardPeriodic with sigma = NaN.
- P1HardPeriodic(Space, double) - Constructor for class etomica.potential.P1HardPeriodic
-
Returns an instance of P1HardPeriodic with the given value of sigma (the
maximum distance between two atoms where they interact)
- P1HardWall - Class in etomica.modules.osmosis
-
- P1HardWall(Space) - Constructor for class etomica.modules.osmosis.P1HardWall
-
- P1HardWall(Space, double) - Constructor for class etomica.modules.osmosis.P1HardWall
-
- P1Harmonic - Class in etomica.potential
-
Potential in which attaches a harmonic spring between each affected atom and
the nearest boundary in each direction.
- P1Harmonic(Space) - Constructor for class etomica.potential.P1Harmonic
-
- P1HarmonicSite - Class in etomica.potential
-
Potential in which attaches a harmonic spring between each affected atom a
nominal site for that atom, as defined by an agent manager.
- P1HarmonicSite(Space) - Constructor for class etomica.potential.P1HarmonicSite
-
- P1HydrogenMielke - Class in etomica.potential
-
- P1HydrogenMielke(Space) - Constructor for class etomica.potential.P1HydrogenMielke
-
- P1HydrogenMielke.P1HydrogenMielkeAtomic - Class in etomica.potential
-
- P1HydrogenMielke.P2HydrogenMielkeAtomic - Class in etomica.potential
-
- P1HydrogenMielkeAtomic(Space) - Constructor for class etomica.potential.P1HydrogenMielke.P1HydrogenMielkeAtomic
-
- P1ImageHarmonic - Class in etomica.freeenergy.npath
-
Created by andrew on 4/11/17.
- P1ImageHarmonic(Space, Vector, double, boolean) - Constructor for class etomica.freeenergy.npath.P1ImageHarmonic
-
- p1ImageHarmonic - Variable in class etomica.freeenergy.npath.SimFe
-
- p1ImageHarmonic - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- p1ImageHarmonic - Variable in class etomica.freeenergy.npath.SimLJ
-
- p1Intra - Variable in class etomica.modules.sam.Sam
-
- P1IntraLambda - Class in etomica.virial
-
- P1IntraLambda(Space, double, P1IntraMolecular, double) - Constructor for class etomica.virial.P1IntraLambda
-
- P1IntraMolecular - Interface in etomica.potential
-
- P1IntraSimple - Class in etomica.potential
-
Generic intramolecular potential group, having one potential for bonded
atoms, and a different potential for unbonded ones.
- P1IntraSimple() - Constructor for class etomica.potential.P1IntraSimple
-
- P1LepsHarmonic - Class in etomica.dimer
-
A combination of the basic LEPS potential describing 3 atoms moving in 1-dimension, paired with a harmonic potential.
- P1LepsHarmonic(Space) - Constructor for class etomica.dimer.P1LepsHarmonic
-
- P1MagicWall - Class in etomica.modules.mu
-
- P1MagicWall(Space, PotentialMasterList) - Constructor for class etomica.modules.mu.P1MagicWall
-
- P1MagneticField - Class in etomica.spin
-
TODO To change the template for this generated type comment go to
Window - Preferences - Java - Code Style - Code Templates
- P1MagneticField(Space) - Constructor for class etomica.spin.P1MagneticField
-
- P1Sinusoidal - Class in etomica.modules.sam
-
- P1Sinusoidal(Space) - Constructor for class etomica.modules.sam.P1Sinusoidal
-
- p1Smash - Variable in class etomica.modules.droplet.Droplet
-
- p1Smash - Variable in class etomica.modules.droplet.DropletAtomic
-
- P1Smash - Class in etomica.modules.droplet
-
Gravity-like potential that pushes the molecules toward the center.
- P1Smash(Space) - Constructor for class etomica.modules.droplet.P1Smash
-
- P1SoftBoundary - Class in etomica.potential
-
- P1SoftBoundary(Space) - Constructor for class etomica.potential.P1SoftBoundary
-
- P1SoftBoundary(Space, double) - Constructor for class etomica.potential.P1SoftBoundary
-
- p1SurfaceBond - Variable in class etomica.modules.sam.Sam
-
- p1Tension - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- P1Tension - Class in etomica.modules.materialfracture
-
- P1Tension(Space) - Constructor for class etomica.modules.materialfracture.P1Tension
-
- P1Tether - Class in etomica.modules.rosmosis
-
Potential for a harmonic tether.
- P1Tether(Box, ISpecies, Space) - Constructor for class etomica.modules.rosmosis.P1Tether
-
- P1Wall - Class in etomica.interfacial
-
- P1Wall(Space, double, double, double) - Constructor for class etomica.interfacial.P1Wall
-
- P1Wall - Class in etomica.modules.adsorption
-
- P1Wall(Space) - Constructor for class etomica.modules.adsorption.P1Wall
-
- P1Wall - Class in etomica.modules.colloid
-
- P1Wall(Space, AtomLeafAgentManager) - Constructor for class etomica.modules.colloid.P1Wall
-
- p1WallA - Variable in class etomica.modules.adsorption.Adsorption
-
- p1WallA - Variable in class etomica.modules.mu.Mu
-
- p1WallB - Variable in class etomica.modules.adsorption.Adsorption
-
- p1WallB - Variable in class etomica.modules.mu.Mu
-
- p1WallColloid - Variable in class etomica.modules.colloid.ColloidSim
-
- p1WallMonomer - Variable in class etomica.modules.colloid.ColloidSim
-
- P1WCAPorousWall - Class in etomica.modules.dcvgcmd
-
This acts as a 1-body WCA potential wall perpendicular to the z direction
with a hole.
- P1WCAPorousWall(Space) - Constructor for class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- P1WCAPorousWall(Space, double, double) - Constructor for class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- P1WCAWall - Class in etomica.modules.dcvgcmd
-
1-D potential that has a WCA form in the Z direction.
- P1WCAWall(Space, int) - Constructor for class etomica.modules.dcvgcmd.P1WCAWall
-
- P1WCAWall(Space, int, double, double) - Constructor for class etomica.modules.dcvgcmd.P1WCAWall
-
- P1WCAWall - Class in etomica.modules.sam
-
1-D potential that has a WCA form in the Z direction.
- P1WCAWall(Space, int) - Constructor for class etomica.modules.sam.P1WCAWall
-
- P1WCAWall(Space, int, double, double) - Constructor for class etomica.modules.sam.P1WCAWall
-
- p2 - Variable in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergiesEAM
-
- p2 - Variable in class etomica.mappedvirial.MeterMeanForce
-
- p2 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
-
- p2 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
-
- p2 - Variable in class etomica.meam.PotentialCalculationEnergySumEAM
-
- p2 - Variable in class etomica.metastable.MeterDensityDistribution
-
- p2 - Variable in class etomica.modules.adsorption.ModifierPMu
-
- p2 - Variable in class etomica.modules.droplet.Droplet
-
- p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- p2 - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- p2 - Variable in class etomica.potential.P2HydrogenPatkowski
-
- p2 - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- p2 - Variable in class etomica.potential.PotentialNonAdditiveDifference
-
- p2 - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
-
- p2 - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
-
- P22CLJQ - Class in etomica.potential
-
Two-centered Lennard Jones molecule with a quadrupole.
- P22CLJQ(Space) - Constructor for class etomica.potential.P22CLJQ
-
- P22CLJQ(Space, double, double, double) - Constructor for class etomica.potential.P22CLJQ
-
- p2AA - Variable in class etomica.modules.adsorption.Adsorption
-
- p2AA - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- p2AA - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- p2AB - Variable in class etomica.modules.adsorption.Adsorption
-
- p2AB - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- P2AceticAcidTwoSite - Class in etomica.models.OPLS
-
- P2AceticAcidTwoSite(double, boolean, int) - Constructor for class etomica.models.OPLS.P2AceticAcidTwoSite
-
- P2Anharmonic - Class in etomica.potential
-
Harmonic Well interatomic potential.
- P2Anharmonic(Space, double) - Constructor for class etomica.potential.P2Anharmonic
-
- P2ArgonAziz1993 - Class in etomica.potential
-
Pair potential for argon from Aziz (1993) JCP 99(6): 4518.
- P2ArgonAziz1993(Space) - Constructor for class etomica.potential.P2ArgonAziz1993
-
- P2ArgonSlavicekEtAl2003 - Class in etomica.potential
-
Ab initio pair potential for argon from Slavicek et al.
- P2ArgonSlavicekEtAl2003(Space) - Constructor for class etomica.potential.P2ArgonSlavicekEtAl2003
-
- P2ArgonTangAndToennies2003 - Class in etomica.potential
-
Pair potential for argon from Tang and Toennies 2003.
- P2ArgonTangAndToennies2003(Space) - Constructor for class etomica.potential.P2ArgonTangAndToennies2003
-
- p2BB - Variable in class etomica.modules.adsorption.Adsorption
-
- p2BB - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- p2BB - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- p2Bond - Variable in class etomica.modules.interfacial.InterfacialSW
-
- p2BondCC - Variable in class etomica.modules.sam.Sam
-
- p2BondCS - Variable in class etomica.modules.sam.Sam
-
- p2CH2 - Variable in class etomica.modules.sam.Sam
-
- p2CH2CH3 - Variable in class etomica.modules.sam.Sam
-
- p2CH2CH3t - Variable in class etomica.modules.sam.Sam
-
- p2CH2Surface - Variable in class etomica.modules.sam.Sam
-
- p2CH2t - Variable in class etomica.modules.sam.Sam
-
- p2CH3 - Variable in class etomica.modules.sam.Sam
-
- p2CH3t - Variable in class etomica.modules.sam.Sam
-
- p2Classy - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
-
- p2Classy - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
-
- p2Classy - Variable in class etomica.potential.P2SemiclassicalAtomic
-
- p2Classy - Variable in class etomica.potential.P2SemiclassicalMolecular
-
- P2CO2EMP - Class in etomica.potential
-
3-point potential for CO2.
- P2CO2EMP(Space, double, double, double, double, double, double, double) - Constructor for class etomica.potential.P2CO2EMP
-
- P2CO2EMP1 - Class in etomica.potential
-
EPM model for CO2.
- P2CO2EMP1(Space) - Constructor for class etomica.potential.P2CO2EMP1
-
- P2CO2EMP2 - Class in etomica.potential
-
EPM2 model for CO2
- P2CO2EMP2(Space) - Constructor for class etomica.potential.P2CO2EMP2
-
- P2CO2H2OSC(double) - Constructor for class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- P2CO2H2OSCTI(double) - Constructor for class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- P2CO2H2OWheatley - Class in etomica.models.co2
-
Ab initio potential for CO2-H2O by Wheatley and Harvey
http://dx.doi.org/10.1063/1.3574345
The CO2 molecule is expected first
- P2CO2H2OWheatley(Space) - Constructor for class etomica.models.co2.P2CO2H2OWheatley
-
- P2CO2H2OWheatley.P2CO2H2OSC - Class in etomica.models.co2
-
- P2CO2H2OWheatley.P2CO2H2OSCTI - Class in etomica.models.co2
-
- P2CO2Hellmann - Class in etomica.models.co2
-
Ab initio potential for CO2-CO2 developed by R.
- P2CO2Hellmann(Space, P2CO2Hellmann.Parameters) - Constructor for class etomica.models.co2.P2CO2Hellmann
-
- P2CO2Hellmann.P2CO2SC - Class in etomica.models.co2
-
- P2CO2Hellmann.Parameters - Enum in etomica.models.co2
-
- P2CO2SC(double) - Constructor for class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- P2CO2TraPPE - Class in etomica.potential
-
I used this original EPM2model to describe TraPPECO2 model
the two models are different in parameters.
- P2CO2TraPPE(Space) - Constructor for class etomica.potential.P2CO2TraPPE
-
- P2Cohesion - Class in etomica.modules.droplet
-
Cohesive potential for mesoscale droplet simulation
- P2Cohesion(Space) - Constructor for class etomica.modules.droplet.P2Cohesion
-
- P2DiscreteFeynmanHibbs - Class in etomica.potential
-
Effective 2 body potential approximating the quantum behavior of atomic
interactions.
- P2DiscreteFeynmanHibbs(Space, Potential2Spherical) - Constructor for class etomica.potential.P2DiscreteFeynmanHibbs
-
- P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum - Class in etomica.potential
-
- P2DLPOLY - Class in etomica.potential
-
- P2DLPOLY(Space) - Constructor for class etomica.potential.P2DLPOLY
-
- P2DoubleWell - Class in etomica.potential
-
Double-well potential.
- P2DoubleWell(Space) - Constructor for class etomica.potential.P2DoubleWell
-
- P2DoubleWell(Space, double, double, double, double) - Constructor for class etomica.potential.P2DoubleWell
-
- P2Dreiding - Class in etomica.potential
-
Dreiding potential.
- P2Dreiding(Space, double, double) - Constructor for class etomica.potential.P2Dreiding
-
- P2EAM - Class in etomica.meam
-
EAM (Embedded Atom Method) potential that pretends to be a pair potential.
- P2EAM(Space, double, double, double, double, double, double, double) - Constructor for class etomica.meam.P2EAM
-
- P2EffectiveFeynmanHibbs - Class in etomica.potential
-
Effective 2 body potential approximating the quantum behavior of atomic
interactions.
- P2EffectiveFeynmanHibbs(Space, Potential2SoftSpherical) - Constructor for class etomica.potential.P2EffectiveFeynmanHibbs
-
- P2Electrostatic - Class in etomica.potential
-
Simple electrostatic potential class.
- P2Electrostatic(Space) - Constructor for class etomica.potential.P2Electrostatic
-
- P2ElectrostaticDreiding - Class in etomica.paracetamol
-
Empirical Isotropic atom-atom repulsion-dispersion potential
Given formula:
U(r) = A*exp(-r/B) - C /r^6
A is in eV
B is in angstrom
C is in eV.angstrom^6
- P2ElectrostaticDreiding(Space) - Constructor for class etomica.paracetamol.P2ElectrostaticDreiding
-
- P2ElectrostaticDreiding(Space, double, double, double) - Constructor for class etomica.paracetamol.P2ElectrostaticDreiding
-
- P2ElectrostaticWithHardCore - Class in etomica.potential
-
Simple electrostatic potential class.
- P2ElectrostaticWithHardCore(Space) - Constructor for class etomica.potential.P2ElectrostaticWithHardCore
-
- P2EwaldReal() - Constructor for class etomica.potential.EwaldSummation.P2EwaldReal
-
- P2Exp6 - Class in etomica.potential
-
Exponential-6 atom-atom repulsion-dispersion potential.
- P2Exp6(Space) - Constructor for class etomica.potential.P2Exp6
-
- P2Exp6(Space, double, double, double) - Constructor for class etomica.potential.P2Exp6
-
- P2Exp6Buckingham - Class in etomica.potential
-
The Buckingham Exponential-6 atom-atom dispersion potential.
- P2Exp6Buckingham(Space) - Constructor for class etomica.potential.P2Exp6Buckingham
-
- P2Exp6Buckingham(Space, double, double, double, double) - Constructor for class etomica.potential.P2Exp6Buckingham
-
- P2Fene - Class in etomica.potential
-
Finite elastic nonlinear extensible (FENE) spring potential.
- P2Fene(Space) - Constructor for class etomica.potential.P2Fene
-
- P2Fene(Space, double, double) - Constructor for class etomica.potential.P2Fene
-
- P2H2OSC(double) - Constructor for class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- P2HardAssociation - Class in etomica.potential
-
Purely attractive square-well potential with no repulsive core.
- P2HardAssociation(Space) - Constructor for class etomica.potential.P2HardAssociation
-
- P2HardAssociation(Space, double, double) - Constructor for class etomica.potential.P2HardAssociation
-
- P2HardAssociationCone - Class in etomica.potential
-
Lennard-Jones potential with a square-well cone of attraction.
- P2HardAssociationCone(Space) - Constructor for class etomica.potential.P2HardAssociationCone
-
- P2HardAssociationCone(Space, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationCone
-
- P2HardAssociationConeDoubleSites - Class in etomica.potential
-
Lennard-Jones potential with a square-well cone of attraction.
- P2HardAssociationConeDoubleSites(Space, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeDoubleSites
-
- P2HardAssociationConeFourSites - Class in etomica.potential
-
Lennard-Jones potential with a square-well cone of attraction.
- P2HardAssociationConeFourSites(Space, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeFourSites
-
- P2HardAssociationConeFourSitesSW - Class in etomica.potential
-
Square-Well cone of attraction for associating fluid theory
Four association sites
- P2HardAssociationConeFourSitesSW(Space, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeFourSitesSW
-
- P2HardAssociationConeOneSite - Class in etomica.potential
-
Lennard-Jones potential with a square-well cone of attraction.
- P2HardAssociationConeOneSite(Space) - Constructor for class etomica.potential.P2HardAssociationConeOneSite
-
- P2HardAssociationConeOneSite(Space, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeOneSite
-
- P2HardAssociationConeReference - Class in etomica.potential
-
potential with a square-well cone of attraction for reference system.
- P2HardAssociationConeReference(Space, double) - Constructor for class etomica.potential.P2HardAssociationConeReference
-
- P2HardAssociationConeReferenceFourSites - Class in etomica.potential
-
potential with a square-well cone of attraction for reference system.
- P2HardAssociationConeReferenceFourSites(Space, double) - Constructor for class etomica.potential.P2HardAssociationConeReferenceFourSites
-
- P2HardAssociationConeSW - Class in etomica.potential
-
Square-Well cone of attraction for associating fluid theory
double association sites
- P2HardAssociationConeSW(Space, double, double, double, double) - Constructor for class etomica.potential.P2HardAssociationConeSW
-
- P2HardAssociationGCPMReference - Class in etomica.models.water
-
- P2HardAssociationGCPMReference(Space, boolean) - Constructor for class etomica.models.water.P2HardAssociationGCPMReference
-
- P2HardAssociationRefAceticAcidTwoSite - Class in etomica.models.OPLS
-
- P2HardAssociationRefAceticAcidTwoSite() - Constructor for class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
-
- P2HardBond - Class in etomica.potential
-
Potential that acts like a hard string connecting the centers of two atoms.
- P2HardBond(Space) - Constructor for class etomica.potential.P2HardBond
-
- P2HardBond(Space, double, double, boolean) - Constructor for class etomica.potential.P2HardBond
-
- P2HardBondedList - Class in etomica.potential
-
Hard potential that wraps two others.
- P2HardBondedList(Simulation, PotentialHard, PotentialHard) - Constructor for class etomica.potential.P2HardBondedList
-
- P2HardBondedList.BondArrayList - Class in etomica.potential
-
- P2HardSphere - Class in etomica.potential
-
Basic hard-(rod/disk/sphere) potential.
- P2HardSphere(Space) - Constructor for class etomica.potential.P2HardSphere
-
- P2HardSphere(Space, double, boolean) - Constructor for class etomica.potential.P2HardSphere
-
- P2HardSphereMC - Class in etomica.modules.colloid
-
- P2HardSphereMC(Space, AtomLeafAgentManager<? extends IAtomList>) - Constructor for class etomica.modules.colloid.P2HardSphereMC
-
- P2HardWrapper - Class in etomica.potential
-
Hard potential class that wraps another hard potential.
- P2HardWrapper(Space, PotentialHard) - Constructor for class etomica.potential.P2HardWrapper
-
- P2Harmonic - Class in etomica.potential
-
Harmonic Well interatomic potential.
- P2Harmonic(Space, double) - Constructor for class etomica.potential.P2Harmonic
-
- P2Harmonic(Space, double, double) - Constructor for class etomica.potential.P2Harmonic
-
- P2HC2Yukawa - Class in etomica.yukawa
-
Hard-core plus two Yukawa fluid (HC2Yukawa): A Lennard-Jones like potential.
- P2HC2Yukawa(Space) - Constructor for class etomica.yukawa.P2HC2Yukawa
-
- P2HC2Yukawa(Space, double, double) - Constructor for class etomica.yukawa.P2HC2Yukawa
-
- p2Head - Variable in class etomica.modules.interfacial.InterfacialSW
-
- p2HeadHead - Variable in class etomica.modules.interfacial.InterfacialSW
-
- p2HeadTail - Variable in class etomica.modules.interfacial.InterfacialSW
-
- P2HeEmpericalQuantum(Space, P2HePCKLJS, double) - Constructor for class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
-
- P2HePCKLJS - Class in etomica.potential
-
Ab initio pair potential for helium from Przybytek et al.
- P2HePCKLJS(Space) - Constructor for class etomica.potential.P2HePCKLJS
-
- P2HePCKLJS(Space, double) - Constructor for class etomica.potential.P2HePCKLJS
-
- P2HePCKLJS.P2HeQFH - Class in etomica.potential
-
This inner class can calculates the Feynman-Hibbs semiclassical
approximation for the potential.
- P2HePCKLJS.P2HeTI - Class in etomica.potential
-
- P2HeQFH(double) - Constructor for class etomica.potential.P2HePCKLJS.P2HeQFH
-
- P2HeQFH(double) - Constructor for class etomica.potential.P2HeSimplified.P2HeQFH
-
- P2HeSimplified - Class in etomica.potential
-
Simplified pair potential for Helium.
- P2HeSimplified(Space) - Constructor for class etomica.potential.P2HeSimplified
-
- P2HeSimplified.P2HeQFH - Class in etomica.potential
-
This inner class can calculates the Feynman-Hibbs semiclassical
approximation for the potential.
- P2HeSimplified.P2HeTI - Class in etomica.potential
-
- P2HeTI(double) - Constructor for class etomica.potential.P2HePCKLJS.P2HeTI
-
- P2HeTI(double) - Constructor for class etomica.potential.P2HeSimplified.P2HeTI
-
- p2Hinde - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- p2Hinde - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- P2HSDipole - Class in etomica.potential
-
Hard sphere molecule with a dipole sitting at the center.
- P2HSDipole(Space) - Constructor for class etomica.potential.P2HSDipole
-
- P2HSDipole(Space, double) - Constructor for class etomica.potential.P2HSDipole
-
- P2HSDipole(Space, double, double) - Constructor for class etomica.potential.P2HSDipole
-
- P2HSDipole(Space, double, double, double) - Constructor for class etomica.potential.P2HSDipole
-
- P2HydrogenHinde - Class in etomica.potential
-
- P2HydrogenHinde(Space) - Constructor for class etomica.potential.P2HydrogenHinde
-
- P2HydrogenHinde.P2HydrogenHindeAtomic - Class in etomica.potential
-
- P2HydrogenHinde.P2HydrogenHindeMolecular - Class in etomica.potential
-
- P2HydrogenHindeAtomic(Space) - Constructor for class etomica.potential.P2HydrogenHinde.P2HydrogenHindeAtomic
-
- P2HydrogenHindeAtomic - Class in etomica.potential
-
- P2HydrogenHindeAtomic(Space) - Constructor for class etomica.potential.P2HydrogenHindeAtomic
-
- P2HydrogenHindeMolecular(Space) - Constructor for class etomica.potential.P2HydrogenHinde.P2HydrogenHindeMolecular
-
- P2HydrogenHindePatkowski - Class in etomica.potential
-
- P2HydrogenHindePatkowski(Space) - Constructor for class etomica.potential.P2HydrogenHindePatkowski
-
- P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiAtomic - Class in etomica.potential
-
- P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiMolecular - Class in etomica.potential
-
- P2HydrogenHindePatkowskiAtomic(Space) - Constructor for class etomica.potential.P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiAtomic
-
- P2HydrogenHindePatkowskiAtomic - Class in etomica.potential
-
- P2HydrogenHindePatkowskiAtomic(Space) - Constructor for class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- P2HydrogenHindePatkowskiMolecular(Space) - Constructor for class etomica.potential.P2HydrogenHindePatkowski.P2HydrogenHindePatkowskiMolecular
-
- P2HydrogenMielkeAtomic(Space) - Constructor for class etomica.potential.P1HydrogenMielke.P2HydrogenMielkeAtomic
-
- P2HydrogenPatkowski - Class in etomica.potential
-
- P2HydrogenPatkowski(Space) - Constructor for class etomica.potential.P2HydrogenPatkowski
-
- P2HydrogenPatkowski.P2HydrogenPatkowskiAtomic - Class in etomica.potential
-
- P2HydrogenPatkowski.P2HydrogenPatkowskiMolecular - Class in etomica.potential
-
- P2HydrogenPatkowskiAtomic(Space) - Constructor for class etomica.potential.P2HydrogenPatkowski.P2HydrogenPatkowskiAtomic
-
- P2HydrogenPatkowskiAtomic - Class in etomica.potential
-
- P2HydrogenPatkowskiAtomic(Space) - Constructor for class etomica.potential.P2HydrogenPatkowskiAtomic
-
- P2HydrogenPatkowskiIso - Class in etomica.potential
-
- P2HydrogenPatkowskiIso(Space) - Constructor for class etomica.potential.P2HydrogenPatkowskiIso
-
- P2HydrogenPatkowskiMolecular(Space) - Constructor for class etomica.potential.P2HydrogenPatkowski.P2HydrogenPatkowskiMolecular
-
- P2Ideal - Class in etomica.potential
-
Ideal-gas two-body potential, which defines no interactions and zero energy
for all pairs given to it.
- P2Ideal(Space) - Constructor for class etomica.potential.P2Ideal
-
- P2LennardJones - Class in etomica.potential
-
Lennard-Jones interatomic potential.
- P2LennardJones(Space) - Constructor for class etomica.potential.P2LennardJones
-
- P2LennardJones(Space, double, double) - Constructor for class etomica.potential.P2LennardJones
-
- P2LennardJonesDreiding - Class in etomica.potential
-
Dreiding: Lennard-Jones non-bonding potential.
- P2LennardJonesDreiding(Space) - Constructor for class etomica.potential.P2LennardJonesDreiding
-
- P2LennardJonesDreiding(Space, double, double) - Constructor for class etomica.potential.P2LennardJonesDreiding
-
- p2LJ - Variable in class etomica.modules.droplet.DropletAtomic
-
- p2LJ - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- p2LJ - Variable in class etomica.normalmode.SimLJVacancy
-
- p2lj - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- p2lj - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- P2LJDipole - Class in etomica.potential
-
Lennard Jones molecule with a point dipole sitting in the center.
- P2LJDipole(Space, double, double, double, double) - Constructor for class etomica.potential.P2LJDipole
-
- P2LJDipole - Class in etomica.rotation
-
r^-12 potential plus a point dipole, force shifted, as used in
Kol, Laird and Leimkuhler, JCP 107 (1997) 2580-2588.
- P2LJDipole(Space) - Constructor for class etomica.rotation.P2LJDipole
-
- P2LJDipole(Space, double, double, double) - Constructor for class etomica.rotation.P2LJDipole
-
- p2LJQ - Variable in class etomica.modules.vle.VLESim
-
- P2LJQ - Class in etomica.potential
-
Lennard Jones molecule with a quadrupole.
- P2LJQ(Space) - Constructor for class etomica.potential.P2LJQ
-
- P2LJQ(Space, double, double, double) - Constructor for class etomica.potential.P2LJQ
-
- P2LJQQ - Class in etomica.potential
-
Lennard Jones molecule with a quadrupole.
- P2LJQQ(Space) - Constructor for class etomica.potential.P2LJQQ
-
- P2LJQQ(Space, double, double, double) - Constructor for class etomica.potential.P2LJQQ
-
- p2LJt - Variable in class etomica.modules.droplet.DropletAtomic
-
- p2mc - Variable in class etomica.modules.colloid.ColloidSim
-
- p2mc - Variable in class etomica.modules.colloid.NeighborListManagerColloid
-
- p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- p2Mix - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- p2mm - Variable in class etomica.modules.colloid.ColloidSim
-
- P2ModifiedMorse - Class in etomica.potential
-
- P2ModifiedMorse(Space) - Constructor for class etomica.potential.P2ModifiedMorse
-
- P2ModifiedMorse(Space, double, double, double, double, double, double) - Constructor for class etomica.potential.P2ModifiedMorse
-
- P2MoleculeMonatomic - Class in etomica.potential
-
- P2MoleculeMonatomic(IPotentialAtomic) - Constructor for class etomica.potential.P2MoleculeMonatomic
-
- P2MoleculeSoftTruncatedSwitched - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2MoleculeSoftTruncatedSwitched(IPotentialMolecularTorque, double, Space) - Constructor for class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- P2MoleculeTruncated - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2MoleculeTruncated(IPotentialMolecular, double, Space, IMoleculePositionDefinition) - Constructor for class etomica.potential.P2MoleculeTruncated
-
- P2Morse - Class in etomica.potential
-
- P2Morse(Space) - Constructor for class etomica.potential.P2Morse
-
- P2Morse(Space, double, double, double) - Constructor for class etomica.potential.P2Morse
-
- p2N2HellmannA - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- P2N2QFH(double) - Constructor for class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- P2Nitrogen - Class in etomica.models.nitrogen
-
P2 6-point potential for Nitrogen.
- P2Nitrogen(Space, double) - Constructor for class etomica.models.nitrogen.P2Nitrogen
-
- P2NitrogenAB - Class in etomica.models.nitrogen
-
P2 6-point potential for Nitrogen.
- P2NitrogenAB(Space, double) - Constructor for class etomica.models.nitrogen.P2NitrogenAB
-
- P2NitrogenAnisotropic - Class in etomica.models.nitrogen
-
P2 6-point potential for Nitrogen with anisotropic contribution
Reference: 1.
- P2NitrogenAnisotropic(Space, double) - Constructor for class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- P2NitrogenHellmann - Class in etomica.potential
-
- P2NitrogenHellmann(Space) - Constructor for class etomica.potential.P2NitrogenHellmann
-
- P2NitrogenHellmann.P2N2QFH - Class in etomica.potential
-
- P2NitrogenShellModel - Class in etomica.models.nitrogen
-
CAUTION!!!!!! The potential DOES NOT really describe the ALPHA and GAMMA structure at
NON-ZERO temperature condition!!
(through observation [SimulationGraphic]
and pressure calculation[MeterPressureMolecular])
P2 shell-model potential for Nitrogen.
- P2NitrogenShellModel(Space, double) - Constructor for class etomica.models.nitrogen.P2NitrogenShellModel
-
- P2O2Bartolomei - Class in etomica.potential
-
- P2O2Bartolomei(Space) - Constructor for class etomica.potential.P2O2Bartolomei
-
- P2O2Bartolomei.P2O2TI - Class in etomica.potential
-
- P2O2TI(double) - Constructor for class etomica.potential.P2O2Bartolomei.P2O2TI
-
- p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- p2Other - Variable in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- p2Patkowski - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- p2Patkowski - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- P2PenetrableBond - Class in etomica.potential
-
Potential with a well having a finite potential on either side.
- P2PenetrableBond(Space) - Constructor for class etomica.potential.P2PenetrableBond
-
- P2PenetrableBond(Space, double, double, boolean) - Constructor for class etomica.potential.P2PenetrableBond
-
- P2PenetrableCar(Space, ParseObj, Box) - Constructor for class etomica.modules.render.RenderMD.P2PenetrableCar
-
- P2PenetrableSphere - Class in etomica.potential
-
Basic penetrable-sphere potential.
- P2PenetrableSphere(Space) - Constructor for class etomica.potential.P2PenetrableSphere
-
Constructor with default values of unity for core diameter and core energy.
- P2PenetrableSphere(Space, double, double) - Constructor for class etomica.potential.P2PenetrableSphere
-
- P2PenetrableSquareWell - Class in etomica.potential
-
Square-well potential with a penetrable core.
- P2PenetrableSquareWell(Space) - Constructor for class etomica.potential.P2PenetrableSquareWell
-
- P2PenetrableSquareWell(Space, double, double, double, boolean) - Constructor for class etomica.potential.P2PenetrableSquareWell
-
- p2pseudo - Variable in class etomica.modules.colloid.ColloidSim
-
- p2pseudo - Variable in class etomica.modules.colloid.NeighborListManagerColloid
-
- P2QChem - Class in etomica.potential
-
This class requires a bash script called ./runQChem to load the appropriate Q-Chem module and run it.
- P2QChem(Space) - Constructor for class etomica.potential.P2QChem
-
- P2QChemInterpolated - Class in etomica.potential
-
Pair potential for argon interpolated from Q-Chem results.
- P2QChemInterpolated(Space) - Constructor for class etomica.potential.P2QChemInterpolated
-
- P2QChemInterpolated.DampingParams - Class in etomica.potential
-
- P2ReactionFieldDipole - Class in etomica.potential
-
Potential to implement the reaction field treatment of electrostatic interactions.
- P2ReactionFieldDipole(Space, IMoleculePositionDefinition) - Constructor for class etomica.potential.P2ReactionFieldDipole
-
- P2ReactionFieldDipoleTruncated - Class in etomica.potential
-
- P2ReactionFieldDipoleTruncated(Space, IMoleculePositionDefinition) - Constructor for class etomica.potential.P2ReactionFieldDipoleTruncated
-
- P2ReactionFieldDipoleTruncated.P0ReactionField - Class in etomica.potential
-
A 0-body potential that should be added along with this potential.
- P2RepRowley - Class in etomica.models.rowley
-
Purely repulsive potential from Rowley et al (2006) used for interactions between satellite sites, X.
- P2RepRowley(Space) - Constructor for class etomica.models.rowley.P2RepRowley
-
- P2RepRowley(Space, double, double) - Constructor for class etomica.models.rowley.P2RepRowley
-
- P2RoughSphere - Class in etomica.potential
-
Basic hard-(rod/disk/sphere) potential, with surface roughness to couple rotation and translational motions.
- P2RoughSphere(Space) - Constructor for class etomica.potential.P2RoughSphere
-
- P2RoughSphere(Space, double, boolean) - Constructor for class etomica.potential.P2RoughSphere
-
- p2S - Variable in class etomica.modules.sam.Sam
-
- p2SCH2 - Variable in class etomica.modules.sam.Sam
-
- p2SCH2t - Variable in class etomica.modules.sam.Sam
-
- P2SemiclassicalAtomic - Class in etomica.potential
-
Effective semiclassical molecular potential using the approach of Takahashi and Imada
- P2SemiclassicalAtomic(Space, IPotentialTorque, double) - Constructor for class etomica.potential.P2SemiclassicalAtomic
-
- P2SemiclassicalAtomic.AtomInfo - Interface in etomica.potential
-
- P2SemiclassicalMolecular - Class in etomica.potential
-
Effective semiclassical molecular potential using the approach of
Takahashi and Imada
http://dx.doi.org/10.1143/JPSJ.53.3765
as described by Schenter
http://dx.doi.org/10.1063/1.1505441
- P2SemiclassicalMolecular(Space, IPotentialMolecularTorque) - Constructor for class etomica.potential.P2SemiclassicalMolecular
-
- P2SemiclassicalMolecular.MoleculeInfo - Interface in etomica.potential
-
- P2SemiclassicalMolecular.MoleculeInfoBrute - Class in etomica.potential
-
- p2Soft - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- p2Soft - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- p2Soft - Variable in class etomica.potential.Potential2SoftSphericalLS
-
- P2SoftSphere - Class in etomica.potential
-
Soft-sphere interatomic potential.
- P2SoftSphere(Space) - Constructor for class etomica.potential.P2SoftSphere
-
- P2SoftSphere(Space, double, double, int) - Constructor for class etomica.potential.P2SoftSphere
-
- P2SoftSphericalTruncated - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2SoftSphericalTruncated(Space, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncated
-
- P2SoftSphericalTruncated.P0Lrc - Class in etomica.potential
-
Inner class that implements the long-range correction for this truncation scheme.
- P2SoftSphericalTruncatedForceShifted - Class in etomica.potential
-
Soft-spherical potential class that shifts both the potential energy and the
force such that both are 0 at the cutoff.
- P2SoftSphericalTruncatedForceShifted(Space, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncatedForceShifted
-
- P2SoftSphericalTruncatedShifted - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2SoftSphericalTruncatedShifted(Space, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncatedShifted
-
- P2SoftSphericalTruncatedSwitched - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2SoftSphericalTruncatedSwitched(Space, Potential2SoftSpherical, double) - Constructor for class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- P2SoftTruncated - Class in etomica.potential
-
Wraps a soft-spherical potential to apply a truncation to it.
- P2SoftTruncated(Potential2Soft, double, Space) - Constructor for class etomica.potential.P2SoftTruncated
-
- P2SpheroPolyhedron - Class in etomica.potential
-
- P2SpheroPolyhedron(Space) - Constructor for class etomica.potential.P2SpheroPolyhedron
-
- P2Spin - Class in etomica.spin
-
Magnetic spin potential, with an energy defined by
U = -J r1 dot r2
where J is a coupling parameter, and r1 and r2 are the vectors given by
atom.coord.position.
- P2Spin(Space) - Constructor for class etomica.spin.P2Spin
-
- P2Spin(Space, double) - Constructor for class etomica.spin.P2Spin
-
- P2SquareWell - Class in etomica.potential
-
Basic square-well potential.
- P2SquareWell(Space) - Constructor for class etomica.potential.P2SquareWell
-
- P2SquareWell(Space, double, double, double, boolean) - Constructor for class etomica.potential.P2SquareWell
-
- P2SquareWellBonded - Class in etomica.modules.chainequilibrium
-
Similar to square-well potential, but considers and alters bonding states
with collisions.
- P2SquareWellBonded(Space, AtomLeafAgentManager, double, double, double) - Constructor for class etomica.modules.chainequilibrium.P2SquareWellBonded
-
- P2SquareWellBonded - Class in etomica.modules.reactionequilibrium
-
Similar to square-well potential, but considers and alters bonding states
with collisions.
- P2SquareWellBonded(Space, AtomLeafAgentManager, double, double, double, boolean) - Constructor for class etomica.modules.reactionequilibrium.P2SquareWellBonded
-
- P2SquareWellBonded.RingResult - Class in etomica.modules.chainequilibrium
-
- P2SquareWellBonding - Class in etomica.modules.catalysis
-
Basic square-well potential.
- P2SquareWellBonding(Space, AtomLeafAgentManager, double, double, double, int, double, double, double) - Constructor for class etomica.modules.catalysis.P2SquareWellBonding
-
- P2SquareWellBondingCO - Class in etomica.modules.catalysis
-
Basic square-well potential.
- P2SquareWellBondingCO(Space, AtomLeafAgentManager, double, double, double, int, double, double, double) - Constructor for class etomica.modules.catalysis.P2SquareWellBondingCO
-
- P2SquareWellMonomer - Class in etomica.modules.colloid
-
- P2SquareWellMonomer(Space, AtomLeafAgentManager) - Constructor for class etomica.modules.colloid.P2SquareWellMonomer
-
- P2SquareWellOneSide - Class in etomica.modules.mu
-
Basic square-well potential.
- P2SquareWellOneSide(Space) - Constructor for class etomica.modules.mu.P2SquareWellOneSide
-
- P2SquareWellOneSide(Space, double, double, double, boolean) - Constructor for class etomica.modules.mu.P2SquareWellOneSide
-
- P2SquareWellRadical - Class in etomica.modules.chainequilibrium
-
Similar to square-well potential, but considers and alters bonding states
with collisions based on free radical reactions.
- P2SquareWellRadical(Space, AtomLeafAgentManager, double, double, double, IRandom) - Constructor for class etomica.modules.chainequilibrium.P2SquareWellRadical
-
- P2SquareWellRobust - Class in etomica.potential
-
Basic square-well potential.
- P2SquareWellRobust(Space) - Constructor for class etomica.potential.P2SquareWellRobust
-
- P2SquareWellRobust(Space, double, double, double, boolean) - Constructor for class etomica.potential.P2SquareWellRobust
-
- P2SquareWellSurface - Class in etomica.modules.catalysis
-
Basic square-well potential.
- P2SquareWellSurface(Space, AtomLeafAgentManager) - Constructor for class etomica.modules.catalysis.P2SquareWellSurface
-
- P2SquareWellSurface(Space, AtomLeafAgentManager, double, double, double, int) - Constructor for class etomica.modules.catalysis.P2SquareWellSurface
-
- p2St - Variable in class etomica.modules.sam.Sam
-
- p2SulfurSurfaceLJ - Variable in class etomica.modules.sam.Sam
-
- p2SurfaceBond - Variable in class etomica.modules.sam.Sam
-
- p2Tail - Variable in class etomica.modules.interfacial.InterfacialSW
-
- p2TailTail - Variable in class etomica.modules.interfacial.InterfacialSW
-
- P2Tether - Class in etomica.potential
-
Potential that acts like a hard string connecting the centers of two atoms.
- P2Tether(Space) - Constructor for class etomica.potential.P2Tether
-
- P2Tether(Space, double, boolean) - Constructor for class etomica.potential.P2Tether
-
- P2TriangleWell - Class in etomica.potential
-
Hard core with an attractive tail that goes to zero linearly with r.
- P2TriangleWell(Space) - Constructor for class etomica.potential.P2TriangleWell
-
- P2TriangleWell(Space, double, double, double) - Constructor for class etomica.potential.P2TriangleWell
-
- p2Truncated - Variable in class etomica.mappedRdf.MappedRdf
-
- p2Truncated - Variable in class etomica.mappedvirial.MappedU
-
- p2Truncated - Variable in class etomica.mappedvirial.MappedVirialLJ
-
- p2Truncated - Variable in class etomica.mappedvirial.MappedVirialLJVGr
-
- p2Truncated - Variable in class etomica.modules.vle.VLESim
-
- P2Water3P - Class in etomica.models.water
-
3-point potential for water.
- P2Water3P(Space, double, double, double, double) - Constructor for class etomica.models.water.P2Water3P
-
- P2Water3PSoft - Class in etomica.models.water
-
3-point potential for water that can calculate gradient and torque (for the
center of mass of the water molecule).
- P2Water3PSoft(Space, double, double, double, double) - Constructor for class etomica.models.water.P2Water3PSoft
-
- P2Water4P - Class in etomica.models.water
-
4-point potential for water.
- P2Water4P(Space, double, double, double, double, IMoleculePositionDefinition) - Constructor for class etomica.models.water.P2Water4P
-
- P2Water4PSoft - Class in etomica.models.water
-
3-point potential for water that can calculate gradient and torque (for the
center of mass of the water molecule).
- P2Water4PSoft(Space, double, double, double, double, IMoleculePositionDefinition) - Constructor for class etomica.models.water.P2Water4PSoft
-
- P2Water4PSoft.AtomicTensorAtomicPair - Interface in etomica.models.water
-
- P2WaterDHS(Space, double, double) - Constructor for class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
-
- P2WaterPotentialsJankowski - Class in etomica.potential
-
- P2WaterPotentialsJankowski(Space, int, int, double, IPotentialAtomic) - Constructor for class etomica.potential.P2WaterPotentialsJankowski
-
- P2WaterSPC - Class in etomica.models.water
-
SPC potential for water.
- P2WaterSPC(Space) - Constructor for class etomica.models.water.P2WaterSPC
-
- P2WaterSPCE - Class in etomica.models.water
-
SPC/E potential for water.
- P2WaterSPCE(Space) - Constructor for class etomica.models.water.P2WaterSPCE
-
- P2WaterSPCSoft - Class in etomica.models.water
-
SPC potential for water.
- P2WaterSPCSoft(Space) - Constructor for class etomica.models.water.P2WaterSPCSoft
-
- P2WaterSzalewicz - Class in etomica.models.water
-
Water potential as described by
http://dx.doi.org/10.1063/1.4875097
This class handles 2-body, 3-body and induction terms.
- P2WaterSzalewicz(Space, int) - Constructor for class etomica.models.water.P2WaterSzalewicz
-
- P2WaterSzalewicz.Component - Enum in etomica.models.water
-
- P2WaterSzalewicz.P2H2OSC - Class in etomica.models.water
-
- P2WaterTIP4P - Class in etomica.models.water
-
TIP4P potential for water.
- P2WaterTIP4P(Space) - Constructor for class etomica.models.water.P2WaterTIP4P
-
- P2WaterTIP4P(Space, double) - Constructor for class etomica.models.water.P2WaterTIP4P
-
- P2WaterTIP4PHardCore - Class in etomica.models.water
-
4-point potential for water.
- P2WaterTIP4PHardCore(Space, double, double, double, double, double) - Constructor for class etomica.models.water.P2WaterTIP4PHardCore
-
- P2WaterTIP4PSoft - Class in etomica.models.water
-
TIP4P potential for water.
- P2WaterTIP4PSoft(Space, double, IMoleculePositionDefinition) - Constructor for class etomica.models.water.P2WaterTIP4PSoft
-
- P2WCA - Class in etomica.potential
-
Weeks-Chandler-Andersen potential.
- P2WCA(Space) - Constructor for class etomica.potential.P2WCA
-
Constructs potential using default sigma and epsilon given by Default class.
- P2WCA(Space, double, double) - Constructor for class etomica.potential.P2WCA
-
- P2XOrder - Class in etomica.normalmode
-
Hard potential that enforces ordering of the x-coordinates of the
pairs.
- P2XOrder(Space, Potential2HardSpherical) - Constructor for class etomica.normalmode.P2XOrder
-
- P2Yukawa - Class in etomica.yukawa
-
Yukawa interatomic potential.
- P2Yukawa(Space) - Constructor for class etomica.yukawa.P2Yukawa
-
- P2Yukawa(Space, double, double) - Constructor for class etomica.yukawa.P2Yukawa
-
- p3 - Variable in class etomica.virial.MayerFunctionMolecularThreeBody
-
- p3 - Variable in class etomica.virial.MayerFunctionSphericalThreeBody
-
- P3AdditiveQChem - Class in etomica.potential
-
- P3AdditiveQChem() - Constructor for class etomica.potential.P3AdditiveQChem
-
- P3AdditiveQChem.DampingParams - Class in etomica.potential
-
- P3AxilrodTeller - Class in etomica.potential
-
Axilrod-Teller potential.
- P3AxilrodTeller(Space, Map<AtomType, P3AxilrodTeller.MyAgent>) - Constructor for class etomica.potential.P3AxilrodTeller
-
- P3AxilrodTeller.MyAgent - Class in etomica.potential
-
- p3Bond - Variable in class etomica.modules.sam.Sam
-
- P3BondAngle - Class in etomica.potential
-
Simple 3-body soft bond-angle potential
- P3BondAngle(Space) - Constructor for class etomica.potential.P3BondAngle
-
- P3BondAngleDreiding - Class in etomica.potential
-
Simple 3-body soft bond-angle for Dreiding potential
* U(theta) = gamma * [ cos(theta) - cos(theta_e)]^2
where gamma is the potential's energy parameter
theta_e is the equilibrium bond angle
- P3BondAngleDreiding(Space, double, double) - Constructor for class etomica.potential.P3BondAngleDreiding
-
- P3CPSNonAdditiveHe - Class in etomica.potential
-
Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
- P3CPSNonAdditiveHe(Space) - Constructor for class etomica.potential.P3CPSNonAdditiveHe
-
- P3CPSNonAdditiveHeLessSimplified - Class in etomica.potential
-
Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
- P3CPSNonAdditiveHeLessSimplified(Space) - Constructor for class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- P3CPSNonAdditiveHeOrig - Class in etomica.potential
-
Ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
- P3CPSNonAdditiveHeOrig(Space) - Constructor for class etomica.potential.P3CPSNonAdditiveHeOrig
-
- P3CPSNonAdditiveHeSimplified - Class in etomica.potential
-
Simplified version of ab initio, non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz JCP 131 064105 2009.
- P3CPSNonAdditiveHeSimplified(Space) - Constructor for class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- P3GCPMAxilrodTeller(Space) - Constructor for class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- P3GCPMAxilrodTeller(Space) - Constructor for class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- P3HydrogenATM - Class in etomica.potential
-
- P3HydrogenATM(Space) - Constructor for class etomica.potential.P3HydrogenATM
-
- P3HydrogenATM.P3HydrogenAtomic - Class in etomica.potential
-
- P3HydrogenAtomic(Space) - Constructor for class etomica.potential.P3HydrogenATM.P3HydrogenAtomic
-
- P3HydrogenGarberoglioMolecular - Class in etomica.potential
-
- P3HydrogenGarberoglioMolecular(Space) - Constructor for class etomica.potential.P3HydrogenGarberoglioMolecular
-
- P3HydrogenManzhos - Class in etomica.potential
-
- P3HydrogenManzhos(Space) - Constructor for class etomica.potential.P3HydrogenManzhos
-
- P3HydrogenManzhos.P3HydrogenManzhosMolecular - Class in etomica.potential
-
- P3HydrogenManzhosMolecular(Space) - Constructor for class etomica.potential.P3HydrogenManzhos.P3HydrogenManzhosMolecular
-
- P3Induction - Class in etomica.potential
-
3-body induction potential based on form used by Oakley and Wheatley.
- P3Induction(Space, Map<AtomType, P3Induction.MyAgent>) - Constructor for class etomica.potential.P3Induction
-
- P3Induction.MyAgent - Class in etomica.potential
-
- p3N2HellmannA - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- p3N2HellmannA - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- P3NitrogenHellmannNonAdditive - Class in etomica.potential
-
- P3NitrogenHellmannNonAdditive(Space) - Constructor for class etomica.potential.P3NitrogenHellmannNonAdditive
-
- p3ParametersFile - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- P3QChem - Class in etomica.potential
-
- P3QChem() - Constructor for class etomica.potential.P3QChem
-
- P3QChem.DampingParams - Class in etomica.potential
-
- p4BondCCCC - Variable in class etomica.modules.sam.Sam
-
- p4BondCCCS - Variable in class etomica.modules.sam.Sam
-
- P4BondTorsion - Class in etomica.potential
-
Torsion potential.
- P4BondTorsion(Space, double, double, double, double) - Constructor for class etomica.potential.P4BondTorsion
-
- P4BondTorsionAlkaneXCCH - Class in etomica.potential
-
slight modification from P4BondTorsion class(change energyAtAngle method)
Siepmann's Alkane TraPPE-EH model, XCCH torsion potential, X can be H or C, H is for H on CH3 only
U(torsion) = Cx * (1 -cos(3phi)); C(C):854K, C(H):717K
- P4BondTorsionAlkaneXCCH(Space, double, double, double, double) - Constructor for class etomica.potential.P4BondTorsionAlkaneXCCH
-
- P4BondTorsionOPLS - Class in etomica.potential
-
OPLS Torsion potential.
- P4BondTorsionOPLS(Space, double, double, double, double) - Constructor for class etomica.potential.P4BondTorsionOPLS
-
- P4TorsionDreiding - Class in etomica.potential
-
Simple 4-body soft bond-angle for Dreiding potential
U(phi) = (1/2) * Vjk * {1 - cos [njk (phi - phiEq)]}
where Vjk is the rotation barrier (always +ve) [unit Kelvin]
njk is the periodicity (an integer)
phiEq is the equilibrium dihedral angle [unit radians]
- P4TorsionDreiding(Space, double, double, int) - Constructor for class etomica.potential.P4TorsionDreiding
-
- pac - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- PadeApproximation - Class in etomica.math.numerical
-
Class to approximate a power series with rational function (Pade Approximation)
Pade[K/L] = A_K/ C_L = B_M
with Kth, Lth and Mth order, where K + L = M
a0 + a1*x + a2*x^2 + ...
- PadeApproximation(double[], int, int) - Constructor for class etomica.math.numerical.PadeApproximation
-
- PadeApproximation.VirialParam - Class in etomica.math.numerical
-
- paint(Graphics) - Method in class etomica.graphics.DisplayCanvas
-
- paint(Graphics) - Method in class etomica.graphics.DisplayScrollingGraph
-
- paint() - Method in class etomica.modules.clustergenerator.ClusterPanel
-
- paint() - Method in class etomica.modules.clustergenerator.Plot
-
Classes which inherit from Plot must define this method.
- paint(Graphics) - Method in class etomica.modules.clustergenerator.Plot
-
- paint(Graphics) - Method in class etomica.util.Grabber.ImagePanel
-
- paintComponent(Graphics) - Method in class etomica.graphics.EtomicaPlot
-
- pair - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- pair - Variable in class etomica.association.BiasVolumeAceticAcid
-
- pair - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- pair - Variable in class etomica.atom.iterator.ApiIndexList
-
- pair - Variable in class etomica.atom.iterator.ApiInnerVariable
-
- pair - Variable in class etomica.atom.iterator.ApiIntergroup
-
- pair - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- pair - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- pair - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- pair - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- pair - Variable in class etomica.models.co2.PNCO2GCPM
-
- pair - Variable in class etomica.models.co2.PNGCPM
-
- pair - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- pair - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- pair - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- pair - Variable in class etomica.models.water.PNWaterGCPM
-
- pair - Variable in class etomica.molecule.iterator.MpiInnerVariable
-
- pair - Variable in class etomica.nbr.list.molecule.NeighborListManagerSlantyMolecular
-
- pair - Variable in class etomica.nbr.list.NeighborListManagerSlanty
-
- pair - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- pair - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- pair - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- pair - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- pair - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- pair - Variable in class etomica.potential.PotentialNonAdditiveDifference
-
- pair - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
-
- pair - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
-
- pairAB - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- pairAB - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- pairAB - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- pairAgents - Variable in class etomica.models.co2.PNGCPM
-
- pairDone - Variable in class etomica.virial.PotentialCommonAtomic
-
- pairDone - Variable in class etomica.virial.PotentialGroupPI
-
- pairForce(IAtom, IAtom) - Method in class etomica.models.water.P2Water4PSoft
-
- pairId(int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams
-
Returns the pair ID for the given indices (id0, id1, id2)
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- pairMatrix - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- pairOnly - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- pairOnly - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- pairOnly - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- pairOnly - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- pairOnly - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- pairOnly - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- pairOnly - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- pairOnly - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- pairOnly - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- pairPolarization - Variable in class etomica.models.co2.PNGCPM
-
- pairPolarization - Variable in class etomica.models.water.PNWaterGCPM
-
- pairPotential - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- pairPotential - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- pairPotential - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- pairPotentialIndex - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- pairSigma - Variable in class etomica.virial.MCMoveClusterAtomHSChainMix
-
- pairSigma - Variable in class etomica.virial.MCMoveClusterAtomHSTreeMix
-
- pairSum - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyDataCov
-
- pairValues - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- pairValues - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- PALETTE_ALTLOC - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_AMINO - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_CHAIN - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_CPK - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_ENERGY - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_FIXEDTEMP - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_FORMAL_CHARGE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_GROUP - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_INSERTION - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_JMOL - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_MOLECULE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_MONOMER - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_NONE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_PARTIAL_CHARGE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_POLYMER - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_PROPERTY - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_RASMOL - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_SHAPELY - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_STRAIGHTNESS - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_STRUCTURE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_SURFACE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_TEMP - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_TYPE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_VARIABLE - Static variable in class org.jmol.constant.StaticConstants
-
- PALETTE_VOLATILE - Static variable in class org.jmol.constant.StaticConstants
-
- panel - Variable in class etomica.graphics.DeviceBox
-
Displayed panel that holds the label and value
(not yet used; meant to implement to make lightweight display)
- panel - Variable in class etomica.graphics.DisplayPlot
-
- panel - Variable in class etomica.graphics.DisplayTable
-
- panel - Variable in class etomica.graphics.DisplayTextBox
-
Displayed panel that holds the label and value
(not yet used; meant to implement to make lightweight display)
- panel - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- panel - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- PanelMainFrame - Class in etomica.virial.GUI.containers
-
- PanelMainFrame(int, int) - Constructor for class etomica.virial.GUI.containers.PanelMainFrame
-
- panelParentGroup - Variable in class etomica.graphics.DisplayTextBoxesCAE
-
- parab - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- Parallelepiped - Class in etomica.math.geometry
-
A polyhedron composed of three pairs of rectangular faces placed opposite
each other and joined at arbitrary angles.
- Parallelepiped(Space) - Constructor for class etomica.math.geometry.Parallelepiped
-
Default constructor makes a cube of unit size
- Parallelepiped(Space, Vector, Vector, Vector) - Constructor for class etomica.math.geometry.Parallelepiped
-
Constructs a parallelepiped with the given edge vectors.
- Parallelogram - Class in etomica.math.geometry
-
A quadrilateral with opposite sides parallel
.
- Parallelogram(Space) - Constructor for class etomica.math.geometry.Parallelogram
-
Default constructor makes a square of unit size
- Parallelogram(Space, Vector, Vector) - Constructor for class etomica.math.geometry.Parallelogram
-
Constructs a parallelogram with the given edge vectors.
- Parallelotope - Interface in etomica.math.geometry
-
Polytope having parallel faces, and which can be specified via a set of edge vectors.
- Param() - Constructor for class etomica.AlkaneEH.CH4NVT.Param
-
- Param() - Constructor for class etomica.AlkaneEH.DHS_NVT.Param
-
- Param() - Constructor for class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- Param() - Constructor for class etomica.dielectric.DHS_NVT.Param
-
- Param() - Constructor for class etomica.dielectric.DLJ_NVT_1site.Param
-
- Param() - Constructor for class etomica.dielectric.TIP4P_NVT.Param
-
- param - Variable in class etomica.modules.interfacial.FitTanh
-
- param - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- param - Variable in class etomica.surfacetension.FitTanh
-
- PARAM_ALL - Static variable in class etomica.graph.operations.MaxIsomorph
-
Parameters instance which does not filter out any graph property.
- PARAM_ROOTY - Static variable in class etomica.graph.operations.MaxIsomorph
-
- ParameterBase - Class in etomica.util
-
Base class for all parameter wrapper implementations.
- ParameterBase() - Constructor for class etomica.util.ParameterBase
-
- parameterGraphic() - Method in class etomica.graphics.DevicePlotPoints
-
Returns the panel that contains the parameter sliders.
- ParameterParser - Interface in etomica.util
-
- Parameters - Interface in etomica.graph.operations
-
- parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- parameters - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- parametersB - Variable in class etomica.potential.P2NitrogenHellmann
-
- parametersB - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- ParameterSetMEAM - Class in etomica.meam
-
This class provides the MEAM parameters for the SAC alloy constituents
(Ag, Cu, and Sn) and for the reference structures required for cross
potentials (the pair potentials between atoms of different types).
- ParameterSetMEAM(double, double, double, double, double, double, double, double, double, double, double, double, double, double, double) - Constructor for class etomica.meam.ParameterSetMEAM
-
- params - Variable in class etomica.graph.operations.UnaryChain.ChainParameters
-
- Params() - Constructor for class etomica.meam.EFSTungsten.Params
-
- params - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- Params() - Constructor for class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
-
- params - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- params - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- params3 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- paramsManager - Variable in class etomica.potential.P3AxilrodTeller
-
- paramsManager - Variable in class etomica.potential.P3Induction
-
- paramsMap - Variable in class etomica.server.representations.ConstructionParams
-
- parent - Variable in class etomica.atom.Atom
-
- parentColor - Variable in class etomica.modules.materialfracture.StrainColorScheme
-
- parentGroup - Variable in class etomica.atom.iterator.ApiIndexList
-
- ParmedParser - Class in etomica.parser
-
Class that generates
ParmedStructure objects by invoking
the
ParmEd library and serializing its
Structure object using JSON.
- ParmedParser() - Constructor for class etomica.parser.ParmedParser
-
- ParmedStructure - Class in etomica.parser
-
Class that contains the data from a
ParmEd Structure,
and has methods to load this data into various
etomica components.
- parse(String) - Method in class etomica.graph.engine.impl.ParserImpl
-
- parse(String) - Method in interface etomica.graph.engine.Parser
-
- parse(String, ParsePosition) - Method in class etomica.util.ScientificFormat
-
Parse out a number from the given text and return it as a Long if
possible; otherwise, return it as a Double.
- parseARGB(String) - Method in class etomica.graph.view.rasterizer.Main.ColorOptionHandler
-
Parse the input value, which should be in the following
format: a.r.g.b where a, r, g and b are integer values,
in decimal notation, between 0 and 255.
- ParseArgs - Class in etomica.util
-
Class that handles parsing of commandline arguments.
- ParseArgs() - Constructor for class etomica.util.ParseArgs
-
- ParseArgs(ParameterBase) - Constructor for class etomica.util.ParseArgs
-
- parseArgs(String[]) - Method in class etomica.util.ParseArgs
-
Parses each argument and attempts to match it with a field from
parameterWrapper and sets the field to the value from the next argument.
- parseArgs(String[], boolean) - Method in class etomica.util.ParseArgs
-
- parseAsDecimal(String, ParsePosition) - Method in class etomica.util.ScientificFormat
-
parse the input string, interpreting it as regular decimal format.
- parseAsExponential(String, ParsePosition) - Method in class etomica.util.ScientificFormat
-
parse the input string, interpreting it as exponential format.
- parseAsFlexible(String, ParsePosition) - Method in class etomica.util.ScientificFormat
-
parse the input string, interpreting it as either regular decimal
format or exponential format.
- parseFloatArray(String) - Static method in class org.jmol.util.Parser
-
- parseFloatArray2d(String) - Static method in class org.jmol.util.Parser
-
- parseFloatArray3d(String) - Static method in class org.jmol.util.Parser
-
- parseFloatArrayBsData(String[], BitSet, float[]) - Static method in class org.jmol.util.Parser
-
- parseFloatArrayData(String[], float[]) - Static method in class org.jmol.util.Parser
-
parses a string array for floats.
- parseFloatArrayDataN(String[], float[], int) - Static method in class org.jmol.util.Parser
-
parses a string array for floats.
- parseFloatArrayFromMatchAndField(String, BitSet, int, int, int[], int, int, float[], int) - Static method in class org.jmol.util.Parser
-
the major lifter here.
- parseFloatArrayNext(String, int[]) - Static method in class org.jmol.util.Parser
-
- parseFloatNext(String, int[]) - Static method in class org.jmol.util.Parser
-
- parseFloatRange(String, int, int[]) - Static method in class org.jmol.util.Parser
-
- parseFloatStr(String) - Static method in class org.jmol.util.Parser
-
- parseFloatStrict(String) - Static method in class org.jmol.util.Parser
-
- parseGromacs(File, File) - Static method in class etomica.parser.ParmedParser
-
Parses the given
Gromacs .top and .gro files
using the
ParmEd python library.
- parseGromacsResourceFiles(String, String) - Static method in class etomica.parser.ParmedParser
-
Convenience method to parse gromacs files located in the etomica-core/src/main/resources directory.
- parseInt(String) - Static method in class org.jmol.util.Parser
-
- parseIntNext(String, int[]) - Static method in class org.jmol.util.Parser
-
- parseIntRadix(String, int) - Static method in class org.jmol.util.Parser
-
- parseIntRange(String, int, int[]) - Static method in class org.jmol.util.Parser
-
- ParseObj - Class in etomica.modules.render
-
- ParseObj(String) - Constructor for class etomica.modules.render.ParseObj
-
- ParseObj.BondInfo - Class in etomica.modules.render
-
- Parser - Interface in etomica.graph.engine
-
- parser - Variable in class etomica.modules.render.RenderMD
-
- Parser - Class in org.jmol.util
-
- Parser() - Constructor for class org.jmol.util.Parser
-
- Parser.Assignment - Interface in etomica.graph.engine
-
- Parser.BinaryOp - Interface in etomica.graph.engine
-
- Parser.BinaryOpByte - Interface in etomica.graph.engine
-
- Parser.Command - Interface in etomica.graph.engine
-
- Parser.CommandPropertyValue - Interface in etomica.graph.engine
-
- Parser.CommandValue - Interface in etomica.graph.engine
-
- Parser.CommandVariable - Interface in etomica.graph.engine
-
- Parser.CommandVariableValue - Interface in etomica.graph.engine
-
- Parser.Constructor - Interface in etomica.graph.engine
-
- Parser.ConstructorColored - Interface in etomica.graph.engine
-
- Parser.ConstructorMono - Interface in etomica.graph.engine
-
- Parser.Expression - Interface in etomica.graph.engine
-
- Parser.ParserException - Exception in etomica.graph.engine
-
- Parser.Property - Interface in etomica.graph.engine
-
- Parser.Statement - Interface in etomica.graph.engine
-
- Parser.StrictExpression - Interface in etomica.graph.engine
-
- Parser.UnaryOp - Interface in etomica.graph.engine
-
- Parser.UnaryOpByte - Interface in etomica.graph.engine
-
- Parser.UnaryOpByteMap - Interface in etomica.graph.engine
-
- Parser.UnaryOpColor - Interface in etomica.graph.engine
-
- Parser.UnaryOpThreeColor - Interface in etomica.graph.engine
-
- Parser.UnaryOpTwoByte - Interface in etomica.graph.engine
-
- Parser.Value - Interface in etomica.graph.engine
-
- Parser.Variable - Interface in etomica.graph.engine
-
- parseRect(String) - Method in class etomica.graph.view.rasterizer.Main.RectangleOptionHandler
-
- ParserException(String) - Constructor for exception etomica.graph.engine.Parser.ParserException
-
- ParserException(String, Throwable) - Constructor for exception etomica.graph.engine.Parser.ParserException
-
- ParserImpl - Class in etomica.graph.engine.impl
-
- ParserImpl() - Constructor for class etomica.graph.engine.impl.ParserImpl
-
- ParserLAMMPS - Class in etomica.parser
-
- ParserLAMMPS() - Constructor for class etomica.parser.ParserLAMMPS
-
- ParserLAMMPS.Options - Class in etomica.parser
-
- ParserLAMMPS.Stuff - Class in etomica.parser
-
- ParserLAMMPS.Truncation - Enum in etomica.parser
-
- parsers - Variable in class etomica.util.ParameterBase
-
- parseStringInfestedFloatArray(String, BitSet, float[]) - Static method in class org.jmol.util.Parser
-
parses a "dirty" string for floats.
- parseToken(String) - Static method in class org.jmol.util.Parser
-
- parseTokenNext(String, int[]) - Static method in class org.jmol.util.Parser
-
- parseTokenRange(String, int, int[]) - Static method in class org.jmol.util.Parser
-
- parseTrimmed(String) - Static method in class org.jmol.util.Parser
-
- parseTrimmedAt(String, int) - Static method in class org.jmol.util.Parser
-
- parseTrimmedRange(String, int, int) - Static method in class org.jmol.util.Parser
-
- PARTIAL_CHARGE_COLIX_BLUE - Static variable in class org.jmol.viewer.JmolConstants
-
- PARTIAL_CHARGE_COLIX_RED - Static variable in class org.jmol.viewer.JmolConstants
-
- PARTIAL_CHARGE_COLIX_WHITE - Static variable in class org.jmol.viewer.JmolConstants
-
- PARTIAL_CHARGE_RANGE_SIZE - Static variable in class org.jmol.viewer.JmolConstants
-
- partialcharge - Static variable in class org.jmol.script.Token
-
- partialdots - Static variable in class org.jmol.script.Token
-
- particleCounters - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- particles - Variable in class etomica.atom.iterator.ANIntragroupExchange
-
- PartitionedIterator - Class in etomica.graph.iterators
-
- PartitionedIterator(Map<Character, Byte>, Map<Character, Byte>) - Constructor for class etomica.graph.iterators.PartitionedIterator
-
- partitions - Variable in class etomica.virial.ClusterSinglyConnected
-
- partitionsA - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- partitionsC - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- PartitionsP - Class in etomica.veos.bigdecimal
-
Number of partitions.
- PartitionsP() - Constructor for class etomica.veos.bigdecimal.PartitionsP
-
Default constructor initializing a list of partitions up to 7.
- partnerColor - Variable in class etomica.graphics.ColorSchemeColliders
-
Color applied to the upList atom of the colliding pair
- partners - Variable in class etomica.atom.iterator.ApiIndexList
-
- partners - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
-
- pascal() - Static method in class etomica.potential.P2O2Bartolomei
-
- Pascal - Class in etomica.units
-
The Pascal unit of pressure, equal to 1 N/m^2.
- path - Static variable in class org.jmol.script.Token
-
- pathforallfiles - Static variable in class org.jmol.script.Token
-
- pause() - Method in class etomica.action.activity.ActivityGroupParallel
-
- pause() - Method in class etomica.action.activity.ActivityGroupSeries
-
Requests a pause in the performance of the actions.
- pause() - Method in class etomica.action.Activity
-
Requests that the Activity pause its execution.
- pause - Static variable in class org.jmol.script.Token
-
- pauseAfterEachAction - Variable in class etomica.action.activity.ActivityGroupSeries
-
- pauseRequested - Variable in class etomica.action.Activity
-
- pbuf - Variable in class org.jmol.g3d.Graphics3D
-
- pbufT - Variable in class org.jmol.g3d.Graphics3D
-
- pBW - Variable in class etomica.interfacial.LJMC
-
- pBW - Variable in class etomica.interfacial.LJMD
-
- pc - Variable in class etomica.action.ActionMinimizeEnergy
-
- pc - Variable in class etomica.data.meter.MeterPressureTensor
-
- pc - Variable in class etomica.data.meter.MeterRDFPC
-
- pc - Variable in class etomica.freeenergy.npath.DataSourceEnergies
-
- pc - Variable in class etomica.interfacial.MeterWallForce
-
- pc - Variable in class etomica.liquidLJ.MeterPUCut
-
- pc - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- pc - Variable in class etomica.mappedvirial.MeterMappedU
-
- pc - Variable in class etomica.mappedvirial.MeterMappedVirial
-
- pc - Variable in class etomica.mappedvirial.MeterMappedVirialV
-
- pc - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- pc - Variable in class etomica.modules.materialfracture.MeterLoad
-
- pc - Variable in class etomica.modules.materialfracture.MeterStress
-
- pc - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pc - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
-
- pc - Variable in class etomica.modules.sam.MeterWallPressure
-
- pc - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- pc - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- pc - Variable in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- pCalc(int, double[], double) - Method in class etomica.veos.QSeries
-
Computes the pressure via dlnQ/dV based on the volume series for Q given by coeffQ.
- pCalc(double, double) - Method in class etomica.veos.Ushcats
-
- pcDADv2 - Variable in class etomica.liquidLJ.MeterPUCut
-
- pcDADv2 - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- pcDUDW - Variable in class etomica.freeenergy.npath.DataSourceEnergies
-
- pCenter - Variable in class etomica.normalmode.MeterDDP
-
- pCenter - Variable in class etomica.normalmode.MeterDP
-
- pcForce - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- pcForce - Variable in class etomica.mappedvirial.MeterMappedU
-
- pcForce - Variable in class etomica.mappedvirial.MeterMappedVirial
-
- pcForce - Variable in class etomica.mappedvirial.MeterMappedVirialV
-
- pcForce - Variable in class etomica.mappedvirial.MeterMeanForce
-
- pcForce - Variable in class etomica.surfacetension.SurfaceTensionMapped
-
- pcForceSum - Variable in class etomica.normalmode.MeterDADB
-
- pcForceSum - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- pcGB - Variable in class etomica.dimer.SimDimerMEAMGB
-
- PCopy - Class in etomica.graph.operations
-
- PCopy() - Constructor for class etomica.graph.operations.PCopy
-
- pCore - Variable in class etomica.virial.MCMoveClusterAtomSQWChain
-
- pCore - Variable in class etomica.virial.MCMoveClusterAtomSQWTree
-
- pCross - Variable in class etomica.normalmode.HSNPT
-
- pdbaddhydrogens - Static variable in class org.jmol.script.Token
-
- pdbgetheader - Static variable in class org.jmol.script.Token
-
- pdbsequential - Static variable in class org.jmol.script.Token
-
- PDBWriter - Class in etomica.action
-
Action that dumps a box's configuration to an PDB file.
- PDBWriter() - Constructor for class etomica.action.PDBWriter
-
- PDBWriter(Box) - Constructor for class etomica.action.PDBWriter
-
- PDF - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PDF_CODE - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PDF_EXTENSION - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PDF_STR - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PE(IData) - Method in interface etomica.data.IData
-
Plus-equals (+=) operation.
- PE(double) - Method in interface etomica.data.IData
-
Plus-equals (+=) operation, adding given value to all values in data.
- PE(IData) - Method in class etomica.data.types.DataDouble
-
Plus-equals (+=) operation.
- PE(double) - Method in class etomica.data.types.DataDouble
-
Plus-equals (+=) operation.
- PE(IData) - Method in class etomica.data.types.DataDoubleArray
-
Plus-equals (+=) operation.
- PE(double) - Method in class etomica.data.types.DataDoubleArray
-
Plus-equals (+=) operation.
- PE(IData) - Method in class etomica.data.types.DataDoubleBDArray
-
Plus-equals (+=) operation.
- PE(double) - Method in class etomica.data.types.DataDoubleBDArray
-
Plus-equals (+=) operation.
- PE(IData) - Method in class etomica.data.types.DataGroup
-
- PE(double) - Method in class etomica.data.types.DataGroup
-
- PE(IData) - Method in class etomica.data.types.DataTensor
-
Plus-equals (+=) operation.
- PE(double) - Method in class etomica.data.types.DataTensor
-
Plus-equals (+=) operation.
- PE(IData) - Method in class etomica.data.types.DataVector
-
Plus-equals (+=) operation.
- PE(double) - Method in class etomica.data.types.DataVector
-
Plus-equals (+=) operation.
- PE(Quaternion) - Method in class etomica.math.Quaternion
-
Adds the input Quaternion components to its components.
- PE(double) - Method in interface etomica.space.Tensor
-
"Plus equals" (+=) operation, adding the given value to each element of this tensor
- PE(Tensor) - Method in interface etomica.space.Tensor
-
"Plus equals" (+=) operation, adding the elements of the given tensor to the
respective elements of this tensor
- PE(int, int, double) - Method in interface etomica.space.Tensor
-
"Plus equals" (+=) operation, performed on a single element of this tensor.
- PE(Vector) - Method in interface etomica.space.Vector
-
Plus-equals (+=) operation.
- PE(double) - Method in interface etomica.space.Vector
-
Plus-equals (+=) operation, causing a constant value to be added to all
components of this vector.
- PE(double) - Method in class etomica.space1d.Tensor1D
-
- PE(int, int, double) - Method in class etomica.space1d.Tensor1D
-
- PE(Tensor) - Method in class etomica.space1d.Tensor1D
-
- PE(double) - Method in class etomica.space1d.Vector1D
-
- PE(Vector) - Method in class etomica.space1d.Vector1D
-
- PE(double) - Method in class etomica.space2d.Tensor2D
-
- PE(Tensor) - Method in class etomica.space2d.Tensor2D
-
- PE(int, int, double) - Method in class etomica.space2d.Tensor2D
-
- PE(Vector) - Method in class etomica.space2d.Vector2D
-
- PE(double) - Method in class etomica.space2d.Vector2D
-
- PE(double) - Method in class etomica.space3d.Tensor3D
-
- PE(Tensor) - Method in class etomica.space3d.Tensor3D
-
- PE(int, int, double) - Method in class etomica.space3d.Tensor3D
-
- PE(Vector) - Method in class etomica.space3d.Vector3D
-
- PE(double) - Method in class etomica.space3d.Vector3D
-
- PE(double) - Method in class etomica.spaceNd.TensorND
-
- PE(Tensor) - Method in class etomica.spaceNd.TensorND
-
- PE(int, int, double) - Method in class etomica.spaceNd.TensorND
-
- PE(Vector) - Method in class etomica.spaceNd.VectorND
-
- PE(double) - Method in class etomica.spaceNd.VectorND
-
- PE(IBigValue) - Method in class etomica.veos.BigValue
-
Plus-equals (+=) operation.
- PE(IBigValue) - Method in interface etomica.veos.IBigValue
-
Plus-equals (+=) operation.
- PE(IBigValue) - Method in class etomica.veos.MyBigDecimal
-
Plus-equals (+=) operation.
- PEa1Tt1(double, Tensor) - Method in interface etomica.space.Tensor
-
"Plus equals" (+=) operation based on a scalar and tensor.
- PEa1Tt1(double, Tensor) - Method in class etomica.space1d.Tensor1D
-
- PEa1Tt1(double, Tensor) - Method in class etomica.space2d.Tensor2D
-
- PEa1Tt1(double, Tensor) - Method in class etomica.space3d.Tensor3D
-
- PEa1Tt1(double, Tensor) - Method in class etomica.spaceNd.TensorND
-
- PEa1Tv1(double, Vector) - Method in interface etomica.space.Vector
-
Increments (+=) components by (a1 * v1)
- PEa1Tv1(double, Vector) - Method in class etomica.space1d.Vector1D
-
- PEa1Tv1(double, Vector) - Method in class etomica.space2d.Vector2D
-
- PEa1Tv1(double, Vector) - Method in class etomica.space3d.Vector3D
-
- PEa1Tv1(double, Vector) - Method in class etomica.spaceNd.VectorND
-
- PEa1Tv1(double, IBigValue) - Method in class etomica.veos.BigValue
-
Plus-equals (+=) a1 times v1.
- PEa1Tv1(double, IBigValue) - Method in interface etomica.veos.IBigValue
-
Plus-equals (+=) a1 times v1.
- PEa1Tv1(double, IBigValue) - Method in class etomica.veos.MyBigDecimal
-
Plus-equals (+=) a1 times v1.
- peek() - Method in class etomica.lattice.RectangularLattice.Iterator
-
- peek() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Returns the next iterate without advancing the iterator.
- peek() - Method in interface etomica.lattice.SiteIterator
-
Returns the next iterate without advancing the iterator.
- pendingActions - Variable in class etomica.action.activity.ActivityGroupSeries
-
- Percent - Class in etomica.units
-
Decimal representation of something that represents the fractional
amount of a whole (e.g., mole fraction) as a percentage value typically
between 0 and 100.
- percent - Static variable in class org.jmol.script.Token
-
- percentvdwatom - Static variable in class org.jmol.script.Token
-
- PercusYevick - Class in etomica.virial
-
Calculates the Percus-Yevick (PY) virial coefficients of second to Mth order for any spherically-symmetric Mayer function, fr.
- PercusYevick() - Constructor for class etomica.virial.PercusYevick
-
- PercusYevick1QC - Class in etomica.virial
-
Computes the Percus-Yevick compressibility-route approximation to the
first quantum correction of Bn, where the first quantum correction is
as defined Kim and Henderson (1968,1966).
- PercusYevick1QC() - Constructor for class etomica.virial.PercusYevick1QC
-
- periodicity - Variable in class etomica.nbr.cell.Api1ACell
-
- periodicity - Variable in class etomica.nbr.cell.ApiAACell
-
- periodicity - Variable in class etomica.nbr.cell.molecule.Mpi1ACell
-
- periodicity - Variable in class etomica.nbr.cell.molecule.MpiAACell
-
- periodicity - Variable in class etomica.nbr.site.Api1ASite
-
- PermutationDegenerateIterator - Class in etomica.math.discrete
-
Iterator that returns unique permutations of an array of integers, with
degeneracy such that some of the integers may appear more than once in the array.
- PermutationDegenerateIterator(int) - Constructor for class etomica.math.discrete.PermutationDegenerateIterator
-
Constructs instance whose iterates are int[] of length n.
- PermutationIterator - Class in etomica.math.discrete
-
Iterator that returns different permutations of a sequence of integers when
called in successive iterations.
- PermutationIterator(int) - Constructor for class etomica.math.discrete.PermutationIterator
-
- PermutationIterator - Class in etomica.virial.cluster
-
- PermutationIterator(int[]) - Constructor for class etomica.virial.cluster.PermutationIterator
-
- permutations - Variable in class etomica.virial.ClusterBonds
-
- Permutator - Interface in etomica.graph.model
-
- perParticleFrequency - Variable in class etomica.integrator.mcmove.MCMoveBox
-
Flag indicating whether nominal frequency is interpreted as a
perParticleFrequency, or as a full frequency.
- perspective(int, float) - Method in class g3dsys.control.G3DSys
-
Handles perspective based on depth and diameter.
- perspectivedepth - Static variable in class org.jmol.script.Token
-
- perspectivemodel - Static variable in class org.jmol.script.Token
-
- pEst - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- PEv1v2(Vector, Vector) - Method in interface etomica.space.Tensor
-
"Plus equals" (+=) operation with a dyad argument.
- PEv1v2(Vector, Vector) - Method in class etomica.space1d.Tensor1D
-
- PEv1v2(Vector, Vector) - Method in class etomica.space2d.Tensor2D
-
- PEv1v2(Vector, Vector) - Method in class etomica.space3d.Tensor3D
-
- PEv1v2(Vector, Vector) - Method in class etomica.spaceNd.TensorND
-
- pFast - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- pFF - Variable in class etomica.interfacial.LJMC
-
- pFF - Variable in class etomica.interfacial.LJMD
-
- pFull - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- pFull - Variable in class etomica.potential.PotentialNonAdditiveDifference
-
- pHarmonic - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- pHarmonic - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- phaseAngles - Variable in class etomica.normalmode.NormalModesVariable
-
- phi(int, double) - Static method in class etomica.densityofstate.CopyOfOrthogonalPolynomial
-
- phi(int, double, double) - Static method in class etomica.densityofstate.OrthogonalPolynomial
-
- PHI - Static variable in class etomica.meam.PotentialMEAM
-
- phi - Static variable in class org.jmol.script.Token
-
- phi2Sum - Variable in class etomica.normalmode.MeterTiltRotationStdev
-
- phiData - Variable in class etomica.data.meter.MeterDihedralAngle
-
- phiEq - Variable in class etomica.potential.P4TorsionDreiding
-
- phiSlider - Variable in class etomica.modules.sam.SamGraphic
-
- phiSum - Variable in class etomica.normalmode.MeterTiltRotationStdev
-
- phongexponent - Static variable in class org.jmol.script.Token
-
- phongExponent - Static variable in class org.jmol.util.Shader
-
- pi - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- pi(MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Euler's constant.
- pi(BigInteger) - Method in class etomica.veos.bigdecimal.Prime
-
return the count of primes <= n
- pi32 - Static variable in class etomica.freeenergy.npath.SimLattice
-
- picking - Static variable in class org.jmol.script.Token
-
- pickingspinrate - Static variable in class org.jmol.script.Token
-
- pickingstyle - Static variable in class org.jmol.script.Token
-
- picklabel - Static variable in class org.jmol.script.Token
-
- Picosecond - Class in etomica.units
-
Simulation unit of time.
- pidOf(Object) - Static method in enum org.jmol.constant.EnumPalette
-
- PINK - Static variable in class org.jmol.util.Colix
-
- PistonCylinder - Class in etomica.modules.pistoncylinder
-
Simple hard-sphere MD in piston-cylinder apparatus
- PistonCylinder(int) - Constructor for class etomica.modules.pistoncylinder.PistonCylinder
-
- PistonCylinderGraphic - Class in etomica.modules.pistoncylinder
-
- PistonCylinderGraphic(PistonCylinder, Space) - Constructor for class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
Creates a PistonCylinder graphic instance.
- PistonCylinderGraphic.Applet - Class in etomica.modules.pistoncylinder
-
- PistonCylinderGraphic.ModifierAtomDiameter - Class in etomica.modules.pistoncylinder
-
- PistonCylinderGraphic.ModifierPistonDensity - Class in etomica.modules.pistoncylinder
-
- PistonPlane - Class in etomica.modules.pistoncylinder
-
Wrap a P1HardMovingBoundary and make it look like a Plane.
- PistonPlane(Space, P1HardMovingBoundary) - Constructor for class etomica.modules.pistoncylinder.PistonPlane
-
- pistonPotential - Variable in class etomica.modules.pistoncylinder.MeterRDFCylinder
-
- pistonPotential - Variable in class etomica.modules.pistoncylinder.PistonCylinder
-
- pistonPotential - Variable in class etomica.modules.pistoncylinder.PistonPlane
-
- pistonUpdateRequested() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
-
- pixel - Variable in class etomica.graphics.DisplayCanvas
-
- Pixel - Class in etomica.units
-
Unit converting between simulation unit of length and pixels rendered in an
image.
- Pixel() - Constructor for class etomica.units.Pixel
-
Constructs with default of 10 pixels per Angstrom.
- Pixel(double) - Constructor for class etomica.units.Pixel
-
Constructor for Pixel.
- pixelUnitToMillimeter - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Millimeters Per Pixel
- pixelX - Variable in class etomica.util.Grabber.CornerData
-
- pixelY - Variable in class etomica.util.Grabber.CornerData
-
- pj - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- pkl - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- pkl - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- pkl - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- PLANCK_H - Static variable in class etomica.util.Constants
-
Planck's constant, in simulation units.
- Plane - Class in etomica.math.geometry
-
Class describing a plane occupying a 3-dimensional space.
- Plane(Space) - Constructor for class etomica.math.geometry.Plane
-
Default constructor returns the y-z plane.
- Plane(Plane) - Constructor for class etomica.math.geometry.Plane
-
Constructs a new Plane as a copy of the given one.
- Plane(Space, double, double, double, double) - Constructor for class etomica.math.geometry.Plane
-
Constructs a Plane satisfying the equation a x + b y + c z + d = 0
- plane - Static variable in class org.jmol.script.Token
-
- PLat - Variable in class etomica.normalmode.MeterSolidProps
-
- PLat - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- Platform - Class in org.jmol.awt
-
- Platform() - Constructor for class org.jmol.awt.Platform
-
- play - Static variable in class org.jmol.script.Token
-
- playDumb - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- playrev - Static variable in class org.jmol.script.Token
-
- plm(int, int, double) - Static method in class etomica.potential.P2O2Bartolomei
-
- plmrb(double[][], double, int) - Method in class etomica.potential.P2HydrogenPatkowski
-
- plmrb(double[][], double, int) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- plot - Variable in class etomica.graphics.DisplayPlot
-
- plot - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- plot - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- plot - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- plot - Variable in class etomica.meam.MEAM_MC
-
- plot - Variable in class etomica.meam.MEAMMd3D
-
- Plot - Class in etomica.modules.clustergenerator
-
Used from comphys.graphic.plot
A class which makes plotting a little more convenient than using
Java's Graphics methods.
- Plot() - Constructor for class etomica.modules.clustergenerator.Plot
-
Constructor sets default size of the plot
- Plot(Color, int, int) - Constructor for class etomica.modules.clustergenerator.Plot
-
- plot - Variable in class etomica.modules.statistics.StatisticsMCGraphic.HistoryPlotBits
-
- plot - Variable in class etomica.simulation.prototypes.LJMD2D
-
- plot - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- plot - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- plot3d - Static variable in class org.jmol.script.Token
-
- plotAction - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- PlotAction(int) - Constructor for class etomica.math.numerical.AkimaSplineSmootherApp.PlotAction
-
- plotAction - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- PlotAction(int) - Constructor for class etomica.math.numerical.AkimaSplineSmootherDyApp.PlotAction
-
- plotBox(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
-
- plotD - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- plotImage(int, int, int, Object, Graphics3D, short, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- plotImage(int, int, int, Image, Graphics3D, short, int, int) - Method in class org.jmol.util.GData
-
- plotImagePixel(int, int, int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- plotLine(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
-
- plotP - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- plotPanel - Variable in class etomica.graphics.SimulationPanel
-
- plotPixelClippedP3i(Point3i) - Method in class org.jmol.g3d.Graphics3D
-
- plotRDF - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- plots - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- plotsPane - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- plotString(String, double, double) - Method in class etomica.modules.clustergenerator.Plot
-
- plotStringCenter(String, double, double) - Method in class etomica.modules.clustergenerator.Plot
-
- plotT - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- plotText(int, int, int, int, int, String, JmolFont, Graphics3D) - Method in class org.jmol.g3d.Graphics3D
-
- plotText(int, int, int, int, int, String, JmolFont, Graphics3D) - Method in class org.jmol.util.GData
-
- plus(Complex) - Method in class etomica.math.Complex
-
Addition of Complex numbers (doesn't change this Complex number).
- plus(Rational) - Method in class etomica.math.Rational
-
Returns a new Rational instance, which is the result of adding the given
Rational to this Rational.
- pmesh - Static variable in class org.jmol.script.Token
-
- pmlt - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- pmlt - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- pN2HellmannA - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- pNA - Variable in class etomica.virial.MayerFunctionNonAdditiveFull
-
- PNCO2GCPM - Class in etomica.models.co2
-
GCPM CO2 potential class (GCPCDO).
- PNCO2GCPM(Space) - Constructor for class etomica.models.co2.PNCO2GCPM
-
- PNCO2GCPM(Space, int) - Constructor for class etomica.models.co2.PNCO2GCPM
-
- PNCO2GCPM.Component - Enum in etomica.models.co2
-
- PNCO2GCPM.P3GCPMAxilrodTeller - Class in etomica.models.co2
-
- PNG - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PNG_CODE - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PNG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PNG_STR - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- PNGCPM - Class in etomica.models.co2
-
Generic GCPM potential class, capable of handling both CO2 and water.
- PNGCPM(Space, Map<AtomType, PNGCPM.GCPMAgent>, int) - Constructor for class etomica.models.co2.PNGCPM
-
- PNGCPM(Space, Map<AtomType, PNGCPM.GCPMAgent>, int, int) - Constructor for class etomica.models.co2.PNGCPM
-
- PNGCPM.Component - Enum in etomica.models.co2
-
- PNGCPM.GCPMAgent - Class in etomica.models.co2
-
- PNGCPM.P3GCPMAxilrodTeller - Class in etomica.models.co2
-
- PNGCPM.PNGCPMCached - Class in etomica.models.co2
-
- PNGCPMCached() - Constructor for class etomica.models.co2.PNGCPM.PNGCPMCached
-
- PNGCPMX - Class in etomica.models.co2
-
GCPM potential that allows combining parameters to be adjusted.
- PNGCPMX(Space, Map<AtomType, PNGCPM.GCPMAgent>, int, double, double, double) - Constructor for class etomica.models.co2.PNGCPMX
-
- PNGCPMX(Space, Map<AtomType, PNGCPM.GCPMAgent>, int, double, double, double, int) - Constructor for class etomica.models.co2.PNGCPMX
-
- PNWaterGCPM - Class in etomica.models.water
-
GCPM Water potential class.
- PNWaterGCPM(Space) - Constructor for class etomica.models.water.PNWaterGCPM
-
- PNWaterGCPM.Component - Enum in etomica.models.water
-
- PNWaterGCPM.PNWaterGCPMCached - Class in etomica.models.water
-
- PNWaterGCPMCached() - Constructor for class etomica.models.water.PNWaterGCPM.PNWaterGCPMCached
-
- PNWaterGCPMThreeSite - Class in etomica.models.water
-
GCPM Water potential with three association site for Wertheim approach.
- PNWaterGCPMThreeSite(Space, double, boolean, boolean) - Constructor for class etomica.models.water.PNWaterGCPMThreeSite
-
- PNWaterGCPMThreeSite(Space, double, boolean) - Constructor for class etomica.models.water.PNWaterGCPMThreeSite
-
- pochhammer(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Pochhammer's function.
- Pochhammer(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
Compute Pochhammer's symbol (this)_n.
- Pochhammer(int) - Method in class etomica.veos.bigdecimal.Rational
-
Compute pochhammer's symbol (this)_n.
- Point - Class in etomica.math.geometry
-
A zero-dimensional polytope, a mathematical point in space.
- Point(Space) - Constructor for class etomica.math.geometry.Point
-
- Point(Space, Vector) - Constructor for class etomica.math.geometry.Point
-
- point - Static variable in class org.jmol.script.Token
-
- Point3f - Class in org.jmol.util
-
A 3 element point that is represented by single precision floating point
x,y,z coordinates.
- Point3f() - Constructor for class org.jmol.util.Point3f
-
- Point3fi - Class in org.jmol.util
-
the Point3fi class allows storage of critical information involving
an atom, picked bond, or measurement point, including:
xyz position
screen position
screen radius (-1 for a simple point)
index (for atoms or for an associated bond that has be picked)
associated modelIndex (for measurement points)
- Point3fi() - Constructor for class org.jmol.util.Point3fi
-
- Point3i - Class in org.jmol.util
-
A 3 element point that is represented by signed integer x,y,z coordinates.
- Point3i() - Constructor for class org.jmol.util.Point3i
-
- Point4f - Class in org.jmol.util
-
A 4 element point that is represented by single precision floating point
x,y,z,w coordinates.
- Point4f() - Constructor for class org.jmol.util.Point4f
-
Constructs and initializes a Point4f to (0,0,0,0).
- pointCharges - Variable in class etomica.models.rowley.ConformationEthanol
-
- pointCharges - Variable in class etomica.models.rowley.ConformationMethanol
-
- pointCharges - Static variable in class etomica.models.rowley.DimerApproach
-
- pointCharges - Variable in class etomica.models.rowley.SpeciesFactoryEthanol
-
- pointCharges - Variable in class etomica.models.rowley.SpeciesFactoryMethanol
-
- pointCharges - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- pointCount() - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- pointCount() - Method in interface etomica.virial.ClusterAbstract
-
Number of points in the cluster.
- pointCount() - Method in class etomica.virial.ClusterBonds
-
- pointCount() - Method in class etomica.virial.ClusterChainHS
-
- pointCount() - Method in class etomica.virial.ClusterChainSoft
-
- pointCount() - Method in class etomica.virial.ClusterCoupledFlipped
-
- pointCount() - Method in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- pointCount() - Method in class etomica.virial.ClusterCoupledFlippedPartial
-
- pointCount() - Method in class etomica.virial.ClusterDifference
-
- pointCount() - Method in class etomica.virial.ClusterExchange
-
- pointCount() - Method in class etomica.virial.ClusterMultiToSingle
-
- pointCount() - Method in class etomica.virial.ClusterSinglyConnected
-
- pointCount() - Method in class etomica.virial.ClusterSum
-
- pointCount() - Method in class etomica.virial.ClusterSumHS
-
- pointCount() - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- pointCount() - Method in class etomica.virial.ClusterSumPolarizable
-
- pointCount() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- pointCount() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- pointCount() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- pointCount() - Method in class etomica.virial.ClusterTree
-
- pointCount() - Method in class etomica.virial.ClusterWeightAbs
-
- pointCount() - Method in class etomica.virial.ClusterWeightSumWall
-
- pointCount() - Method in class etomica.virial.ClusterWeightUmbrella
-
- pointCount() - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- pointCount() - Method in class etomica.virial.ClusterWheatleyHS
-
- pointCount() - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
-
- pointCount() - Method in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
-
- pointCount() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- pointCount() - Method in class etomica.virial.ClusterWheatleySoft
-
- pointCount() - Method in class etomica.virial.ClusterWheatleySoftBD
-
- pointCount() - Method in class etomica.virial.ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
-
- pointCount() - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
- pointCount() - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
-
- pointCount() - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- pointCount() - Method in class etomica.virial.simulations.VirialH2OGCPMD.Clusterfoo
-
- pointgroupdistancetolerance - Static variable in class org.jmol.script.Token
-
- pointgrouplineartolerance - Static variable in class org.jmol.script.Token
-
- PointsToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.PointsToggler
-
- Poise - Class in etomica.units
-
The Poise unit of viscosity, equal to 1 gram/(cm-sec).
- pol - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- polE1 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- polSite - Variable in class etomica.potential.P3Induction.MyAgent
-
- Polygon - Class in etomica.math.geometry
-
Representation of a mathematical polygon, a 2-dimensional polytope.
- Polygon(Space, int) - Constructor for class etomica.math.geometry.Polygon
-
Constructs a polygon with the given number of sides arranged in a closed loop.
- Polygon(LineSegment[]) - Constructor for class etomica.math.geometry.Polygon
-
Constructs a polygon using the given edges for its sides.
- polygonColixes - Variable in class org.jmol.util.MeshSurface
-
- polygonCount - Variable in class org.jmol.util.MeshSurface
-
- polygonCount0 - Variable in class org.jmol.util.MeshSurface
-
- PolygonGeneral - Class in etomica.math.geometry
-
TODO To change the template for this generated type comment go to Window -
Preferences - Java - Code Style - Code Templates
- PolygonGeneral(Space, int) - Constructor for class etomica.math.geometry.PolygonGeneral
-
- PolygonGeneral(LineSegment[]) - Constructor for class etomica.math.geometry.PolygonGeneral
-
- polygonIndexes - Variable in class org.jmol.util.MeshSurface
-
- polyhedra - Static variable in class org.jmol.script.Token
-
- Polyhedron - Class in etomica.math.geometry
-
Representation of a mathematical polyhedron, a 3-dimensional polytope.
- Polyhedron(Polygon[]) - Constructor for class etomica.math.geometry.Polyhedron
-
Constructs a polyhedron with the given faces for its sides.
- PolyhedronGeneral - Class in etomica.math.geometry
-
Representation of a mathematical polyhedron, a 3-dimensional polytope.
- PolyhedronGeneral(Polygon[]) - Constructor for class etomica.math.geometry.PolyhedronGeneral
-
- polymer - Static variable in class org.jmol.script.Token
-
- polymerlength - Static variable in class org.jmol.script.Token
-
- polymerList - Variable in class etomica.modules.sam.CriterionTether3
-
- polymerSpecies - Variable in class etomica.modules.sam.CriterionTether3
-
- PolynomialFit - Class in etomica.math.numerical
-
Class that performs a polynomial fit to x,y data, optionally taking weights
associated with each data point.
- PolynomialFit() - Constructor for class etomica.math.numerical.PolynomialFit
-
- polytope - Variable in class etomica.graphics.DisplayPolytope
-
- Polytope - Class in etomica.math.geometry
-
Representation of a mathematical polytope, which is a finite region of space
enclosed by a finite number of hyperplanes.
- Polytope(Polytope[]) - Constructor for class etomica.math.geometry.Polytope
-
Constructs a polytope of dimension D from the D-1 finite "planes" that
constitute it.
- populate(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperBranched
-
- populate(AtomArrayList, IAtom, IAtom, boolean) - Method in class etomica.association.AssociationHelperDouble
-
- populate(MoleculeArrayList, IMolecule, boolean) - Method in class etomica.association.AssociationHelperMolecule
-
- populateArrays(int, boolean) - Method in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
-
- populateArrays(int, boolean) - Method in class etomica.overlap.DataOverlap
-
- populateBonds(Graph, List<ClusterBonds>, List<Double>, boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- populateEFBonds(Graph, List<ClusterBonds>, List<Double>, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- populateEFBonds(Graph, List<ClusterBonds>, List<Double>, int, int, boolean, boolean, int) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- populateEFBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- populateEFdfdTBonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- populateEFdfdTdf2dT2Bonds(Graph, ArrayList<ClusterBonds>, boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- populateList(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperBranched
-
- populateList(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperDouble
-
- populateList(MoleculeArrayList, IMolecule, boolean) - Method in class etomica.association.AssociationHelperMolecule
-
- populateList(AtomArrayList, IAtom, boolean) - Method in class etomica.association.AssociationHelperSingle
-
- populateList(AtomArrayList, IAtom, boolean) - Method in interface etomica.association.IAssociationHelper
-
Populates smerList with all atoms in the smer that contains atom.
- populateList(MoleculeArrayList, IMolecule, boolean) - Method in interface etomica.association.IAssociationHelperMolecule
-
Populates smerList with all molecules in the smer that contains molecule.
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveAtomMonomer
-
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveAtomSmer
-
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveBiasUB
-
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveRotateAssociated
-
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveSmer
-
- populateList(AtomArrayList) - Method in class etomica.association.MCMoveSmerRotate
-
- populateList(AtomArrayList, IAtom) - Method in class etomica.association.MCMoveVolumeAssociated
-
- populateVDWDiameters(DiameterHashByElement) - Static method in class etomica.atom.DiameterHashByElement
-
Populates the given instance with diameters based on atomic radii
(taken from various sources).
- PopupListener(JPopupMenu) - Constructor for class etomica.graphics.DisplayPlot.PopupListener
-
- popupMenu - Variable in class etomica.graphics.DisplayPlot.PopupListener
-
- poreCenter - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- pos - Variable in class etomica.models.co2.P2CO2Hellmann
-
- pos - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- pos - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- pos - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- pos - Variable in class etomica.normalmode.MeterPlaneSlip
-
- pos - Variable in class etomica.potential.P2NitrogenHellmann
-
- pos - Variable in class etomica.potential.P3HydrogenGarberoglioMolecular
-
- pos - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- posA - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- posB - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- position - Variable in class etomica.atom.Atom
-
- position - Variable in class etomica.data.meter.MeterProfileByAtoms
-
- position - Variable in class etomica.data.meter.MeterProfileByVolume
-
- position - Variable in class etomica.math.geometry.Polytope
-
- position - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- position(IMolecule) - Method in interface etomica.molecule.IMoleculePositionDefinition
-
Returns the defined position for the given molecule.
- position - Variable in class etomica.molecule.MoleculeOriented
-
- position(IMolecule) - Method in class etomica.molecule.MoleculePositionCOM
-
- position(IMolecule) - Method in class etomica.molecule.MoleculePositionFirstAtom
-
- position(IMolecule) - Method in class etomica.molecule.MoleculePositionGeometricCenter
-
- position(IMolecule) - Method in class etomica.molecule.MoleculePositionGeometricCenterAlkaneEH
-
- position(IMolecule) - Method in class etomica.molecule.MoleculePositionGeometricCenterPBC
-
- position - Variable in class etomica.normalmode.MeterDisplacementMoleculeRMS
-
- positionDefinition(IMolecule) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- positionDefinition - Variable in class etomica.config.ConfigurationLattice
-
- positionDefinition - Variable in class etomica.data.meter.MeterProfileByVolume
-
- positionDefinition - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
-
- positionDefinition - Variable in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- positionDefinition - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- positionDefinition - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- positionDefinition - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- positionDefinition - Variable in class etomica.models.water.P2Water4P
-
- positionDefinition - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- positionDefinition - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- positionDefinition - Variable in class etomica.modules.rosmosis.MeterFlux
-
- positionDefinition - Variable in class etomica.modules.sam.Sam
-
- positionDefinition - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- positionDefinition - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- positionDefinition - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- positionDefinition - Variable in class etomica.nbr.cell.NeighborCellManager
-
- positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource
-
- positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
-
- positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
-
- positionDefinition - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- positionDefinition - Variable in class etomica.potential.P2MoleculeTruncated
-
- positionDefinition - Variable in class etomica.potential.P2ReactionFieldDipole
-
- positionDefinition - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- positionDefinition - Variable in class etomica.potential.PotentialGroupSoft
-
- positionDefinition - Variable in class etomica.virial.ClusterCoupledFlipped
-
- positionDefinition - Variable in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- positionDefinition - Variable in class etomica.virial.ClusterCoupledFlippedPartial
-
- positionDefinition - Variable in class etomica.virial.CoordinatePairMoleculeSet
-
- positionDefinition - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- positionDefinition - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- positionOld - Variable in class etomica.models.hexane.MCMoveCBMC
-
- positions - Variable in class etomica.dimer.SimDimerLJadatom
-
- positions - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- positions - Variable in class etomica.dimer.SimDimerMEAMGB
-
- positions - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- positions - Variable in class etomica.virial.CoordinatePairLeafSet
-
- positionSelectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- positionSource - Variable in class etomica.data.meter.MeterProfile
-
- positionSource - Variable in class etomica.data.meter.MeterWidomInsertion
-
- positionSource - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- positionSource - Variable in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- positionSource - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- positionSource - Variable in class etomica.liquidLJ.MeterWidomInsertionP
-
- positionSource - Variable in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- positionVector - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- positionVector - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- postAction - Variable in class etomica.action.SimulationRestart
-
- postAction - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- posVec - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- posVecToAtoms(Vector[], Vector[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- pot - Variable in class etomica.virial.PotentialCommonAtomic
-
- poten() - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- potential - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- potential - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- potential - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- potential - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- potential - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- potential - Variable in class etomica.data.meter.MeterEnergy
-
- potential - Variable in class etomica.data.meter.MeterPotentialEnergy
-
- potential - Variable in class etomica.densityofstate.DensityOfState
-
- potential - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
-
- potential - Variable in class etomica.dimer.EnergyMap
-
- potential - Variable in class etomica.dimer.SimDimerLJgb
-
- potential - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- potential - Variable in class etomica.dimer.SimDimerMEAMGB
-
- potential - Variable in class etomica.freeenergy.npath.SimFe
-
- potential - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- potential - Variable in class etomica.freeenergy.npath.SimLJ
-
- potential - Variable in class etomica.integrator.mcmove.MCMove
-
- potential - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- potential - Variable in class etomica.liquidLJ.LjMC3D
-
- potential - Variable in class etomica.liquidLJ.LjMd3D
-
- potential - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- potential - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- potential - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- potential - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potential - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- potential - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- potential - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- potential - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- potential - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- potential - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- potential - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- potential - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- potential - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- potential - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- potential - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- potential - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- potential - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- potential - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- potential - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- potential - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
-
- potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- potential - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
-
- potential - Variable in class etomica.normalmode.LJVacancyMin
-
- potential - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- potential - Variable in class etomica.normalmode.MeterAPIPotentialEnergy
-
- potential - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- potential - Variable in class etomica.normalmode.SimHSMDVacancy
-
- potential - Variable in class etomica.normalmode.SimLJHTTISuper
-
- potential - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- potential - Variable in class etomica.normalmode.SimLJVacancy
-
- potential - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- potential - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- potential - Variable in class etomica.potential.P2MoleculeTruncated
-
- potential - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- potential - Variable in class etomica.potential.P2SoftSphericalTruncated
-
- potential - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- Potential - Class in etomica.potential
-
Superclass for all Potential classes, which define how the atoms in the
system interact with each other.
- Potential(int, Space) - Constructor for class etomica.potential.Potential
-
General constructor for a potential instance
- potential - Variable in class etomica.potential.PotentialGroup.PotentialLinker
-
- potential - Variable in class etomica.potential.PotentialMaster.PotentialLinker
-
- potential - Variable in class etomica.simulation.prototypes.ChainHSMD3D
-
- potential - Variable in class etomica.simulation.prototypes.GEMCWithRotation
-
- potential - Variable in class etomica.simulation.prototypes.HSMD3D
-
The hard-sphere potential governing the interactions.
- potential - Variable in class etomica.simulation.prototypes.HSMD3DNoNbr
-
- potential - Variable in class etomica.simulation.prototypes.LJMD2D
-
- potential - Variable in class etomica.simulation.prototypes.LJMD3D
-
- potential - Variable in class etomica.simulation.prototypes.SoftSphere3d
-
- potential - Variable in class etomica.simulation.prototypes.SWMD2D
-
- potential - Variable in class etomica.simulation.prototypes.SWMD3D
-
- potential - Variable in class etomica.spin.Heisenberg
-
- potential - Variable in class etomica.tests.TestLJGCMC3D
-
- potential - Variable in class etomica.tests.TestLJMC3D
-
- potential - Variable in class etomica.thermointegration.LjMc3D
-
- potential - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- potential - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- potential - Variable in class etomica.threaded.PotentialThreaded
-
- potential - Variable in class etomica.virial.MayerGeneralAtomic
-
- potential - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- potential - Variable in class etomica.yukawa.TestHC2YukawaMC3D
-
- potential - Variable in class etomica.yukawa.TestYukawaMC3D
-
- potential - Variable in class etomica.yukawa.TestYukawaMD3D
-
- Potential0 - Class in etomica.potential
-
Potential that does not depend on any atom positions.
- Potential0(Space) - Constructor for class etomica.potential.Potential0
-
- Potential0Lrc - Class in etomica.potential
-
Zero-body potential implementing the long-range correction
that compensates for truncation of the potential.
- Potential0Lrc(Space, AtomType[], IPotentialAtomic) - Constructor for class etomica.potential.Potential0Lrc
-
- potential1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- Potential1 - Class in etomica.potential
-
Potential acting on a single atom or atom group.
- Potential1(Space) - Constructor for class etomica.potential.Potential1
-
- Potential1.Intramolecular - Interface in etomica.potential
-
Marker interface indicating that a one-body potential is an intramolecular
potential, and not, e.g., a potential of interaction with an external field.
- potential11 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potential11 - Variable in class etomica.simulation.prototypes.HSMC2D
-
- potential11 - Variable in class etomica.simulation.prototypes.HSMD2D
-
- potential12 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potential12 - Variable in class etomica.simulation.prototypes.HSMC2D
-
- potential12 - Variable in class etomica.simulation.prototypes.HSMD2D
-
- Potential2 - Class in etomica.potential
-
Potential acting on 2 atoms or molecules.
- Potential2(Space) - Constructor for class etomica.potential.Potential2
-
Constructs potential with given space.
- potential22 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potential22 - Variable in class etomica.simulation.prototypes.HSMC2D
-
- potential22 - Variable in class etomica.simulation.prototypes.HSMD2D
-
- Potential2HardSpherical - Class in etomica.potential
-
Methods for a hard (impulsive), spherically-symmetric pair potential.
- Potential2HardSpherical(Space) - Constructor for class etomica.potential.Potential2HardSpherical
-
- Potential2Soft - Interface in etomica.potential
-
Methods for properties obtained for a soft, differentiable pair potential.
- Potential2SoftSpherical - Class in etomica.potential
-
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
- Potential2SoftSpherical(Space) - Constructor for class etomica.potential.Potential2SoftSpherical
-
- Potential2SoftSphericalLS - Class in etomica.potential
-
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
- Potential2SoftSphericalLS(Space, double, double[], Potential2Soft) - Constructor for class etomica.potential.Potential2SoftSphericalLS
-
- Potential2SoftSphericalLSMulti - Class in etomica.liquidLJ
-
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
- Potential2SoftSphericalLSMulti(Space, double[], Potential2Soft) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- Potential2SoftSphericalLSMultiLat - Class in etomica.liquidLJ
-
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
- Potential2SoftSphericalLSMultiLat(Space, double[], Potential2Soft, CoordinateDefinition) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- Potential2SoftSphericalLSMultiLat.ReturnValue - Class in etomica.liquidLJ
-
- Potential2SoftSphericalLSMultiLatSlanty - Class in etomica.liquidLJ
-
Methods for a soft (non-impulsive), spherically-symmetric pair potential.
- Potential2SoftSphericalLSMultiLatSlanty(Space, double[], Potential2Soft, CoordinateDefinition, int[]) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
-
- Potential2Spherical - Interface in etomica.potential
-
interface for spherical 2-body potentials
- potentialA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- potentialA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- potentialA - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- potentialA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- potentialA - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- potentialAA - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- potentialAA - Variable in class etomica.modules.mu.Mu
-
- potentialAA - Variable in class etomica.modules.osmosis.OsmosisSim
-
- potentialAB - Variable in class etomica.modules.mu.Mu
-
- potentialAB - Variable in class etomica.modules.osmosis.OsmosisSim
-
- potentialAddedNotify(IPotentialAtomic, PotentialGroup) - Method in class etomica.nbr.PotentialMasterHybrid
-
- potentialAddedNotify(IPotentialAtomic, PotentialGroup) - Method in class etomica.nbr.PotentialMasterNbr
-
- potentialAddedNotify(IPotentialAtomic, PotentialGroup) - Method in class etomica.potential.PotentialMaster
-
Notifies the PotentialMaster that the sub-potential has been added to
the given PotentialGroup, which is associated (but not necessarily held
by) this PotentialMaster.
- potentialAgentManager - Variable in class etomica.potential.PotentialMasterMonatomic
-
- PotentialAndIterator(IPotentialAtomic, AtomsetIteratorBasisDependent) - Constructor for class etomica.chem.models.Model.PotentialAndIterator
-
- PotentialArray - Class in etomica.potential
-
Instances of this class are created by AtomType classes to
store the list of potentials and criteria that apply to
the atoms of that type.
- PotentialArray() - Constructor for class etomica.potential.PotentialArray
-
- PotentialArrayByType - Class in etomica.potential
-
This class stores an array of Potentials and remembers the "other" IAtomType
that the IPotential applies to.
- PotentialArrayByType() - Constructor for class etomica.potential.PotentialArrayByType
-
- PotentialArrayMolecular - Class in etomica.potential
-
Instances of this class are created by MoleculeType classes to
store the list of potentials and criteria that apply to
the molecules of that type.
- PotentialArrayMolecular() - Constructor for class etomica.potential.PotentialArrayMolecular
-
- potentialAtomic - Variable in class etomica.potential.PotentialMolecularMonatomic
-
- PotentialAtomicSum - Class in etomica.potential
-
Atomic potential class that simply sums up contributions from multiple
(atomic) potentials.
- PotentialAtomicSum(IPotentialAtomic[]) - Constructor for class etomica.potential.PotentialAtomicSum
-
- potentialAtt - Variable in class etomica.virial.MayerPTAtt
-
- potentialAtt - Variable in class etomica.virial.MayerSphericalPTAtt
-
- potentialB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- potentialB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- potentialB - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- potentialB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- potentialB - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- potentialBB - Variable in class etomica.modules.mu.Mu
-
- potentialBB - Variable in class etomica.modules.osmosis.OsmosisSim
-
- potentialBonded - Variable in class etomica.modules.render.RenderMD
-
- PotentialCalculation - Interface in etomica.potential
-
Class defining a particular action to be performed on a set of atoms using an
arbitrary potential.
- PotentialCalculationDUDW - Class in etomica.freeenergy.npath
-
Potential calculation whose sole purpose in life is to invoke getDUDW
Created by andrew on 5/8/17.
- PotentialCalculationDUDW() - Constructor for class etomica.freeenergy.npath.PotentialCalculationDUDW
-
- PotentialCalculationEFSSP - Class in etomica.normalmode
-
- PotentialCalculationEFSSP(Space, Box, CoordinateDefinition, double, double, boolean) - Constructor for class etomica.normalmode.PotentialCalculationEFSSP
-
- PotentialCalculationEnergies() - Constructor for class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- PotentialCalculationEnergiesEAM(P2EAM) - Constructor for class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergiesEAM
-
- PotentialCalculationEnergySum - Class in etomica.potential
-
Evaluates the energy summed over all iterated atoms.
- PotentialCalculationEnergySum() - Constructor for class etomica.potential.PotentialCalculationEnergySum
-
- PotentialCalculationEnergySumBigDecimal - Class in etomica.potential
-
Mimics original PotentialEnergySum calculation, but uses a BigDecimal
representation for the sum.
- PotentialCalculationEnergySumBigDecimal(int) - Constructor for class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
- PotentialCalculationEnergySumCutoff - Class in etomica.liquidLJ
-
Evaluates the energy summed over all iterated atoms.
- PotentialCalculationEnergySumCutoff(Space, double[]) - Constructor for class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
- PotentialCalculationEnergySumEAM - Class in etomica.meam
-
Evaluate the energy for the EAM model using the P2EAM potential.
- PotentialCalculationEnergySumEAM(P2EAM) - Constructor for class etomica.meam.PotentialCalculationEnergySumEAM
-
- PotentialCalculationForcePressureSum - Class in etomica.potential
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationForcePressureSum(Space) - Constructor for class etomica.potential.PotentialCalculationForcePressureSum
-
- PotentialCalculationForcePressureSumGB - Class in etomica.dimer
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationForcePressureSumGB(Space, Box) - Constructor for class etomica.dimer.PotentialCalculationForcePressureSumGB
-
- PotentialCalculationForceStress - Class in etomica.modules.materialfracture
-
- PotentialCalculationForceStress(Space) - Constructor for class etomica.modules.materialfracture.PotentialCalculationForceStress
-
- PotentialCalculationForceSum - Class in etomica.potential
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationForceSum() - Constructor for class etomica.potential.PotentialCalculationForceSum
-
- PotentialCalculationForceSumThreaded - Class in etomica.threaded
-
- PotentialCalculationForceSumThreaded(PotentialCalculationForceSum[], Space) - Constructor for class etomica.threaded.PotentialCalculationForceSumThreaded
-
- PotentialCalculationForceSumWall - Class in etomica.modules.sam
-
- PotentialCalculationForceSumWall(P1WCAWall) - Constructor for class etomica.modules.sam.PotentialCalculationForceSumWall
-
- PotentialCalculationForceSumWallForce - Class in etomica.modules.rosmosis
-
Sums the force and torque on each iterated atom or molecule and adds it to
the agent associated with the atom.
- PotentialCalculationForceSumWallForce(IPotential) - Constructor for class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
-
- PotentialCalculationHyperVirialSum - Class in etomica.potential
-
Evaluates the hypervirial summed over all iterated atoms.
- PotentialCalculationHyperVirialSum() - Constructor for class etomica.potential.PotentialCalculationHyperVirialSum
-
- PotentialCalculationLJSP - Class in etomica.normalmode
-
- PotentialCalculationLJSP(Space, Box, CoordinateDefinition, double, double, double, double, double) - Constructor for class etomica.normalmode.PotentialCalculationLJSP
-
- PotentialCalculationMappedEnergy - Class in etomica.mappedvirial
-
PotentialCalculation that implements mapped-averaged framework (to get the energy).
- PotentialCalculationMappedEnergy(Space, Box, int, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Constructor for class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- PotentialCalculationMappedRdf - Class in etomica.mappedRdf
-
Created by aksharag on 5/16/17.
- PotentialCalculationMappedRdf(Space, Box, int, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Constructor for class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- PotentialCalculationMappedVirial - Class in etomica.mappedvirial
-
PotentialCalculation that implements mapped-averaged virial (to get the
pressure).
- PotentialCalculationMappedVirial(Space, Box, int, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Constructor for class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- PotentialCalculationMappedVirialV - Class in etomica.mappedvirial
-
PotentialCalculation that implements mapped-averaged virial (to get the
pressure).
- PotentialCalculationMappedVirialV(Space, Box, int, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Constructor for class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- PotentialCalculationMappedVirialV.UShift - Class in etomica.mappedvirial
-
- PotentialCalculationMappedVirialV.USine - Class in etomica.mappedvirial
-
- PotentialCalculationMappedVirialV.VFunc - Interface in etomica.mappedvirial
-
- PotentialCalculationMolecular - Interface in etomica.potential
-
Class defining a particular action to be performed on a set of atoms using an
arbitrary potential.
- PotentialCalculationMolecularVirialSum - Class in etomica.potential
-
Evaluates the virial summed over all iterated molecules.
- PotentialCalculationMolecularVirialSum() - Constructor for class etomica.potential.PotentialCalculationMolecularVirialSum
-
- PotentialCalculationPhiSum - Class in etomica.potential
-
- PotentialCalculationPhiSum(Space) - Constructor for class etomica.potential.PotentialCalculationPhiSum
-
- PotentialCalculationPressureTensor - Class in etomica.potential
-
Calculates the pressure tensor by calculating the force on each atom, along
with including the kinetic portion (from the velocities or an Integrator).
- PotentialCalculationPressureTensor(Space) - Constructor for class etomica.potential.PotentialCalculationPressureTensor
-
- PotentialCalculationRDF - Class in etomica.data.meter
-
PotentialCalculation that simply does the work of collecting an RDF.
- PotentialCalculationRDF(Space, Box) - Constructor for class etomica.data.meter.PotentialCalculationRDF
-
- PotentialCalculationSolidSuper - Class in etomica.normalmode
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationSolidSuper(Space, CoordinateDefinition) - Constructor for class etomica.normalmode.PotentialCalculationSolidSuper
-
- PotentialCalculationSolidSuperCut - Class in etomica.normalmode
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationSolidSuperCut(Space, CoordinateDefinition, double[]) - Constructor for class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- PotentialCalculationSolidSuperCutLS - Class in etomica.normalmode
-
Sums the force on each iterated atom and adds it to the integrator agent
associated with the atom.
- PotentialCalculationSolidSuperCutLS(Space, CoordinateDefinition, double[]) - Constructor for class etomica.normalmode.PotentialCalculationSolidSuperCutLS
-
- PotentialCalculationSumCutoff - Class in etomica.liquidLJ
-
Evaluates the energy summed over all iterated atoms.
- PotentialCalculationSumCutoff(Space, double[]) - Constructor for class etomica.liquidLJ.PotentialCalculationSumCutoff
-
- PotentialCalculationSumCutoffLS - Class in etomica.liquidLJ
-
Evaluates the energy summed over all iterated atoms.
- PotentialCalculationSumCutoffLS() - Constructor for class etomica.liquidLJ.PotentialCalculationSumCutoffLS
-
- PotentialCalculationTorqueSum - Class in etomica.potential
-
Sums the force and torque on each iterated atom or molecule and adds it to
the agent associated with the atom.
- PotentialCalculationTorqueSum() - Constructor for class etomica.potential.PotentialCalculationTorqueSum
-
- PotentialCalculationTorqueSumWallForce - Class in etomica.modules.rosmosis
-
Sums the force and torque on each iterated atom or molecule and adds it to
the agent associated with the atom.
- PotentialCalculationTorqueSumWallForce(IPotential) - Constructor for class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
- PotentialCalculationVirialSum - Class in etomica.potential
-
Evaluates the virial summed over all iterated atoms.
- PotentialCalculationVirialSum() - Constructor for class etomica.potential.PotentialCalculationVirialSum
-
- PotentialCalculationWallForce() - Constructor for class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
-
- potentialCC - Variable in class etomica.modules.catalysis.Catalysis
-
- potentialCC - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialCC - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialChoice - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- potentialChooser - Variable in class etomica.modules.insertion.InsertionGraphic
-
- potentialChooser - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- potentialChooser - Variable in class etomica.modules.swmd.SwmdGraphic
-
- potentialChooserListener - Variable in class etomica.modules.insertion.InsertionGraphic
-
- potentialChooserListener - Variable in class etomica.modules.mu.MuGraphic
-
- potentialChooserListener - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- potentialChooserListener - Variable in class etomica.modules.swmd.SwmdGraphic
-
- potentialCHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialCHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialCHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialCHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialCN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialCN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialCO - Variable in class etomica.modules.catalysis.Catalysis
-
- potentialCO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialCO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- PotentialCommonAtomic - Class in etomica.virial
-
- PotentialCommonAtomic(IPotentialAtomic) - Constructor for class etomica.virial.PotentialCommonAtomic
-
- potentialCS - Variable in class etomica.modules.catalysis.Catalysis
-
- potentialCS - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- PotentialCuLREP - Class in etomica.meam
-
- PotentialCuLREP(Space) - Constructor for class etomica.meam.PotentialCuLREP
-
- PotentialDLPOLY - Class in etomica.potential
-
- PotentialDLPOLY(Space) - Constructor for class etomica.potential.PotentialDLPOLY
-
- PotentialEAM - Class in etomica.meam
-
EAM (Embedded Atom Method) potential
- PotentialEAM(Space, double, double, double, double, double, double) - Constructor for class etomica.meam.PotentialEAM
-
- PotentialEAM_LS - Class in etomica.meam
-
EAM (Embedded Atom Potential) potential with a lattice sum
- PotentialEAM_LS(CoordinateDefinition, Space, double, double, double, double, double, double, Vector[]) - Constructor for class etomica.meam.PotentialEAM_LS
-
- PotentialEFS - Class in etomica.meam
-
EFS (Extended Finnis-Sinclair) potential
- PotentialEFS(Space, double, double, double, double, double, double, double, double, double) - Constructor for class etomica.meam.PotentialEFS
-
- PotentialEmul - Class in etomica.potential
-
PotentialEmul class invokes the emul external program to compute energies
between molecules.
- PotentialEmul(Space, String) - Constructor for class etomica.potential.PotentialEmul
-
- PotentialEmul(Space, String, double) - Constructor for class etomica.potential.PotentialEmul
-
- PotentialEmul(Space, String, int, double) - Constructor for class etomica.potential.PotentialEmul
-
- PotentialEmulCached - Class in etomica.virial
-
Potential class whose sole purpose is to remember previously calculated
energies and return them if no change has been made to the configuration.
- PotentialEmulCached(Space, String, int) - Constructor for class etomica.virial.PotentialEmulCached
-
- PotentialEmulCached(Space, String, double, int) - Constructor for class etomica.virial.PotentialEmulCached
-
- PotentialEmulCached(Space, String, int, double, int) - Constructor for class etomica.virial.PotentialEmulCached
-
- potentialES - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- potentialES - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- potentialGhost - Variable in class etomica.modules.insertion.Insertion
-
- PotentialGroup - Class in etomica.potential
-
Collection of potentials that act between the atoms contained in
one or more groups of atoms.
- PotentialGroup(int) - Constructor for class etomica.potential.PotentialGroup
-
Makes a potential group defined on the position of nBody atom or atom groups.
- PotentialGroup(int, Space) - Constructor for class etomica.potential.PotentialGroup
-
- PotentialGroup.PotentialLinker - Class in etomica.potential
-
- PotentialGroup3PI - Class in etomica.virial
-
PotentialGroup that calculates the energy between PI molecules triplets.
- PotentialGroup3PI(int) - Constructor for class etomica.virial.PotentialGroup3PI
-
- PotentialGroup3PI.PotentialGroup3PISkip - Class in etomica.virial
-
- PotentialGroup3PISkip(int) - Constructor for class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
-
- PotentialGroupHybrid - Class in etomica.nbr
-
A PotentialGroup class to work with PotentialMasterHybrid.
- PotentialGroupHybrid(int) - Constructor for class etomica.nbr.PotentialGroupHybrid
-
- PotentialGroupNbr - Class in etomica.nbr
-
- PotentialGroupNbr(int) - Constructor for class etomica.nbr.PotentialGroupNbr
-
- PotentialGroupPI - Class in etomica.virial
-
PotentialGroup that calculates the energy between PI molecule pairs.
- PotentialGroupPI(int) - Constructor for class etomica.virial.PotentialGroupPI
-
- PotentialGroupPI.PotentialGroupPISkip - Class in etomica.virial
-
- PotentialGroupPISkip(int) - Constructor for class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
-
- PotentialGroupSoft - Class in etomica.potential
-
include virial and gradient for a molecular potential
- PotentialGroupSoft(int, Space, double) - Constructor for class etomica.potential.PotentialGroupSoft
-
- PotentialHard - Interface in etomica.potential
-
Interface for hard potentials, having impulsive forces.
- potentialHpHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHpHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialHpN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHpN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialHS - Variable in class etomica.modules.insertion.InsertionGraphic
-
- potentialHS - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- potentialHS - Variable in class etomica.modules.swmd.SwmdGraphic
-
- potentialHyHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHyHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialHyHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHyHy - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialHyN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHyN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialHyO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialHyO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialIdeal - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- potentialIdeal - Variable in class etomica.modules.swmd.SwmdGraphic
-
- potentialLevel - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- potentialLevel - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- potentialLevel - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- potentialLevel - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- PotentialLinker(IPotentialAtomic, AtomsetIteratorBasisDependent, AtomType[], PotentialGroup.PotentialLinker) - Constructor for class etomica.potential.PotentialGroup.PotentialLinker
-
- PotentialLinker(IPotentialMolecular, MoleculesetIteratorPDT, ISpecies[]) - Constructor for class etomica.potential.PotentialMaster.PotentialLinker
-
- potentialList - Variable in class etomica.potential.PotentialMaster
-
- potentialLJ - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- potentialLJClCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialLJLS - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- potentialLJLS - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- potentialLJNaCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialLJNaNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialLJOCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialLJONa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialM1 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potentialM2 - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potentialMaster - Variable in class etomica.action.ActionMinimizeEnergy
-
- potentialMaster - Variable in class etomica.AlkaneEH.CH4NVT
-
- potentialMaster - Variable in class etomica.AlkaneEH.DHS_NVT
-
- potentialMaster - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
-
- potentialMaster - Variable in class etomica.association.MCMoveDimer
-
- potentialMaster - Variable in class etomica.association.MCMoveDimerRotate
-
- potentialMaster - Variable in class etomica.association.MCMoveSmer
-
- potentialMaster - Variable in class etomica.association.MCMoveSmerRotate
-
- potentialMaster - Variable in class etomica.conjugategradient.DerivativeEnergyFunction
-
- potentialMaster - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- potentialMaster - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- potentialMaster - Variable in class etomica.data.meter.MeterHyperVirial
-
- potentialMaster - Variable in class etomica.data.meter.MeterPressure
-
- potentialMaster - Variable in class etomica.data.meter.MeterPressureTensor
-
- potentialMaster - Variable in class etomica.data.meter.MeterRDFPC
-
- potentialMaster - Variable in class etomica.densityofstate.DensityOfState
-
- potentialMaster - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
-
- potentialMaster - Variable in class etomica.dielectric.DHS_NVT
-
- potentialMaster - Variable in class etomica.dielectric.DLJ_NVT_1site
-
- potentialMaster - Variable in class etomica.dielectric.TIP4P_NVT
-
- potentialMaster - Variable in class etomica.dimer.EnergyMap
-
- potentialMaster - Variable in class etomica.dimer.SimDimerLJadatom
-
- potentialMaster - Variable in class etomica.dimer.SimDimerLJgb
-
- potentialMaster - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- potentialMaster - Variable in class etomica.dimer.SimDimerMEAMGB
-
- potentialMaster - Variable in class etomica.freeenergy.npath.DataSourceEnergies
-
- potentialMaster - Variable in class etomica.freeenergy.npath.SimFe
-
- potentialMaster - Variable in class etomica.integrator.IntegratorBox
-
- potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- potentialMaster - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- potentialMaster - Variable in class etomica.interfacial.LJMD
-
- potentialMaster - Variable in class etomica.interfacial.MeterWallForce
-
- potentialMaster - Variable in class etomica.kmc.SimKMCLJadatom
-
- potentialMaster - Variable in class etomica.liquidLJ.MeterPU
-
- potentialMaster - Variable in class etomica.liquidLJ.MeterPUCut
-
- potentialMaster - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- potentialMaster - Variable in class etomica.mappedvirial.MeterMappedU
-
- potentialMaster - Variable in class etomica.mappedvirial.MeterMappedVirial
-
- potentialMaster - Variable in class etomica.mappedvirial.MeterMappedVirialV
-
- potentialMaster - Variable in class etomica.mappedvirial.MeterMeanForce
-
- potentialMaster - Variable in class etomica.math.numerical.CalcGradientDifferentiable
-
- potentialMaster - Variable in class etomica.meam.EFSTungsten
-
- potentialMaster - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- potentialMaster - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- potentialMaster - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- potentialMaster - Variable in class etomica.meam.MEAM_MC
-
- potentialMaster - Variable in class etomica.meam.MEAMMd3D
-
- potentialMaster - Variable in class etomica.metastable.LJmuVT
-
- potentialMaster - Variable in class etomica.metastable.LJNPT
-
- potentialMaster - Variable in class etomica.metastable.LJNVT
-
- potentialMaster - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- potentialMaster - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- potentialMaster - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- potentialMaster - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- potentialMaster - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- potentialMaster - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- potentialMaster - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- potentialMaster - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- potentialMaster - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- potentialMaster - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- potentialMaster - Variable in class etomica.models.rowley.DimerApproach
-
- potentialMaster - Variable in class etomica.models.water.TestEwaldTIP4PWater
-
- potentialMaster - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- potentialMaster - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- potentialMaster - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- potentialMaster - Variable in class etomica.modules.colloid.ColloidSim
-
- potentialMaster - Variable in class etomica.modules.droplet.DropletAtomic
-
- potentialMaster - Variable in class etomica.modules.mu.P1MagicWall
-
- potentialMaster - Variable in class etomica.modules.render.RenderMD
-
- potentialMaster - Variable in class etomica.modules.sam.ConfigurationSAM
-
- potentialMaster - Variable in class etomica.modules.sam.Sam
-
- potentialMaster - Variable in class etomica.modules.vle.MeterPressure2
-
- potentialMaster - Variable in class etomica.nbr.list.BoxAgentSourceCellManagerList
-
- potentialMaster - Variable in class etomica.nbr.list.molecule.BoxAgentSourceCellManagerListMolecular
-
- potentialMaster - Variable in class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
-
- potentialMaster - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource
-
- potentialMaster - Variable in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- potentialMaster - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- potentialMaster - Variable in class etomica.nbr.list.NeighborCellManagerList
-
- potentialMaster - Variable in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
-
- potentialMaster - Variable in class etomica.nbr.list.NeighborListManager
-
- potentialMaster - Variable in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- potentialMaster - Variable in class etomica.normalmode.HessianDB
-
- potentialMaster - Variable in class etomica.normalmode.HSDimerNPT
-
- potentialMaster - Variable in class etomica.normalmode.HSNPT
-
- potentialMaster - Variable in class etomica.normalmode.HTTPSoftSphereSim
-
- potentialMaster - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
-
- potentialMaster - Variable in class etomica.normalmode.LJVacancyMin
-
- potentialMaster - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- potentialMaster - Variable in class etomica.normalmode.MeterDADB
-
- potentialMaster - Variable in class etomica.normalmode.MeterDDP
-
- potentialMaster - Variable in class etomica.normalmode.MeterDP
-
- potentialMaster - Variable in class etomica.normalmode.MeterSolidDA
-
- potentialMaster - Variable in class etomica.normalmode.MeterSolidDACut
-
- potentialMaster - Variable in class etomica.normalmode.MeterSolidProps
-
- potentialMaster - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- potentialMaster - Variable in class etomica.normalmode.MeterTargetTP
-
- potentialMaster - Variable in class etomica.normalmode.MinimizeHCP
-
- potentialMaster - Variable in class etomica.normalmode.NormalModesMolecular
-
- potentialMaster - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- potentialMaster - Variable in class etomica.normalmode.SimCalcSLJ
-
- potentialMaster - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
-
- potentialMaster - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- potentialMaster - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- potentialMaster - Variable in class etomica.normalmode.SimEinStep1
-
- potentialMaster - Variable in class etomica.normalmode.SimEinStep1HCP
-
- potentialMaster - Variable in class etomica.normalmode.SimEinStep2
-
- potentialMaster - Variable in class etomica.normalmode.SimEinStep2HCP
-
- potentialMaster - Variable in class etomica.normalmode.SimFluidSoftSphere
-
- potentialMaster - Variable in class etomica.normalmode.SimLJHTTISuper
-
- potentialMaster - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- potentialMaster - Variable in class etomica.normalmode.SimLJVacancy
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- potentialMaster - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- potentialMaster - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- potentialMaster - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- potentialMaster - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- potentialMaster - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialMaster - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialMaster - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
-
- potentialMaster - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
-
- potentialMaster - Variable in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
-
- potentialMaster - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
-
- potentialMaster - Variable in class etomica.potential.P2SquareWellRobust
-
- potentialMaster - Variable in class etomica.potential.PotentialGroup
-
- PotentialMaster - Class in etomica.potential
-
Manager of all potentials in simulation.
- PotentialMaster() - Constructor for class etomica.potential.PotentialMaster
-
- PotentialMaster(IteratorFactory) - Constructor for class etomica.potential.PotentialMaster
-
- potentialMaster - Variable in class etomica.simulation.prototypes.HSMD3D
-
- potentialMaster - Variable in class etomica.simulation.prototypes.SoftSphere3d
-
- potentialMaster - Variable in class etomica.spin.Heisenberg
-
- potentialMaster - Variable in class etomica.surfacetension.LJMC
-
- potentialMaster - Variable in class etomica.surfacetension.SurfaceTensionMapped
-
- potentialMaster - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- PotentialMaster.AtomIterator0 - Class in etomica.potential
-
- PotentialMaster.MoleculeIterator0 - Class in etomica.potential
-
- PotentialMaster.PotentialLinker - Class in etomica.potential
-
- potentialMasterA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- potentialMasterA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- potentialMasterA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- potentialMasterB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- potentialMasterB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- potentialMasterB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- potentialMasterCell - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- potentialMasterCell - Variable in class etomica.freeenergy.npath.SimLJ
-
- potentialMasterCell - Variable in class etomica.interfacial.LJMC
-
- potentialMasterCell - Variable in class etomica.liquidLJ.LjMC3D
-
- PotentialMasterCell - Class in etomica.nbr.cell
-
A PotentialMaster for use with a Simulation where cell-listing of atoms and
their neighbors is appropriate.
- PotentialMasterCell(Simulation, Space) - Constructor for class etomica.nbr.cell.PotentialMasterCell
-
Creates PotentialMasterCell with default (1.0) range.
- PotentialMasterCell(Simulation, double, Space) - Constructor for class etomica.nbr.cell.PotentialMasterCell
-
Constructs with null AtomPositionDefinition, which indicates the position
definition given with each atom's AtomType should be used.
- PotentialMasterCell(Simulation, double, IMoleculePositionDefinition, Space) - Constructor for class etomica.nbr.cell.PotentialMasterCell
-
- PotentialMasterCell(Simulation, double, BoxAgentSourceCellManager, Space) - Constructor for class etomica.nbr.cell.PotentialMasterCell
-
- PotentialMasterCell(Simulation, double, BoxAgentSourceCellManager, BoxAgentManager<NeighborCellManager>, Space) - Constructor for class etomica.nbr.cell.PotentialMasterCell
-
- potentialMasterCell - Variable in class etomica.nbr.PotentialGroupHybrid
-
- potentialMasterD - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- potentialMasterD - Variable in class etomica.dimer.SimDimerMEAMGB
-
- potentialMasterD - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- potentialMasterDADv2 - Variable in class etomica.liquidLJ.MeterPUCut
-
- potentialMasterDADv2 - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- potentialMasterDADv2 - Variable in class etomica.normalmode.MeterSolidDACut
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep1
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep1HCP
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep2
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimEinStep2HCP
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- potentialMasterHarmonic - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- PotentialMasterHybrid - Class in etomica.nbr
-
PotentialMaster that uses both neighbor-cell iteration and cell-list
iteration.
- PotentialMasterHybrid(Simulation, double, Space) - Constructor for class etomica.nbr.PotentialMasterHybrid
-
Invokes superclass constructor, specifying IteratorFactoryCell
for generating molecule iterators.
- PotentialMasterHybrid(Simulation, IMoleculePositionDefinition, double, Space) - Constructor for class etomica.nbr.PotentialMasterHybrid
-
Constructs class using given position definition for all atom cell assignments.
- potentialMasterList - Variable in class etomica.liquidLJ.LjMd3D
-
- PotentialMasterList - Class in etomica.nbr.list
-
PotentialMaster used to implement neighbor listing.
- PotentialMasterList(Simulation, Space) - Constructor for class etomica.nbr.list.PotentialMasterList
-
Default constructor uses range of 1.0.
- PotentialMasterList(Simulation, double, Space) - Constructor for class etomica.nbr.list.PotentialMasterList
-
Constructor specifying space and range for neighbor listing; uses null AtomPositionDefinition.
- PotentialMasterList(Simulation, double, IMoleculePositionDefinition, Space) - Constructor for class etomica.nbr.list.PotentialMasterList
-
Constructs class using given position definition for all atom cell
assignments.
- PotentialMasterList(Simulation, double, BoxAgentSourceCellManagerList, Space) - Constructor for class etomica.nbr.list.PotentialMasterList
-
- PotentialMasterList(Simulation, double, BoxAgentSourceCellManagerList, BoxAgentManager<? extends BoxCellManager>, Space) - Constructor for class etomica.nbr.list.PotentialMasterList
-
- PotentialMasterList(Simulation, double, BoxAgentSourceCellManagerList, BoxAgentManager<? extends BoxCellManager>, PotentialMasterList.NeighborListAgentSource, Space) - Constructor for class etomica.nbr.list.PotentialMasterList
-
- potentialMasterList - Variable in class etomica.nbr.PotentialGroupHybrid
-
- potentialMasterList - Variable in class etomica.normalmode.SimHSMDVacancy
-
- PotentialMasterList.NeighborListAgentSource - Class in etomica.nbr.list
-
- PotentialMasterListDimer - Class in etomica.dimer
-
- PotentialMasterListDimer(Simulation, Space) - Constructor for class etomica.dimer.PotentialMasterListDimer
-
- PotentialMasterListMolecular - Class in etomica.nbr.list.molecule
-
PotentialMaster used to implement neighbor listing.
- PotentialMasterListMolecular(Simulation, Space) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Default constructor uses range of 1.0.
- PotentialMasterListMolecular(Simulation, double, Space) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Constructor specifying space and range for neighbor listing; uses null AtomPositionDefinition.
- PotentialMasterListMolecular(Simulation, double, IMoleculePositionDefinition, Space) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Constructs class using given position definition for all atom cell
assignments.
- PotentialMasterListMolecular(Simulation, double, BoxAgentSourceCellManagerListMolecular, Space) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- PotentialMasterListMolecular(Simulation, double, BoxAgentSourceCellManagerListMolecular, BoxAgentManager<? extends BoxCellManager>, Space) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- PotentialMasterListMolecular(Simulation, double, BoxAgentSourceCellManagerListMolecular, BoxAgentManager<? extends BoxCellManager>, PotentialMasterListMolecular.NeighborListAgentSourceMolecular, Space) - Constructor for class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- PotentialMasterListMolecular.NeighborListAgentSourceMolecular - Class in etomica.nbr.list.molecule
-
- PotentialMasterListThreaded - Class in etomica.threaded.atom
-
- PotentialMasterListThreaded(Simulation, Space) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(Simulation, Space, double) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(Simulation, Space, double, IMoleculePositionDefinition) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(Simulation, Space, double, BoxAgentSourceCellManagerList) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(Simulation, Space, double, BoxAgentSourceCellManagerList, BoxAgentManager) - Constructor for class etomica.threaded.atom.PotentialMasterListThreaded
-
- PotentialMasterListThreaded - Class in etomica.threaded.domain
-
- PotentialMasterListThreaded(Simulation, Space) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(Simulation, double, Space) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(Simulation, double, IMoleculePositionDefinition, Space) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(Simulation, double, BoxAgentSourceCellManagerList, Space) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
-
- PotentialMasterListThreaded(Simulation, double, BoxAgentSourceCellManagerList, BoxAgentManager<NeighborCellManager>, Space) - Constructor for class etomica.threaded.domain.PotentialMasterListThreaded
-
- PotentialMasterListThreaded.NeighborListAgentSourceThreaded - Class in etomica.threaded.domain
-
- PotentialMasterListWorker - Class in etomica.threaded.atom
-
- PotentialMasterListWorker(int, AtomTypeAgentManager, PotentialMasterListThreaded) - Constructor for class etomica.threaded.atom.PotentialMasterListWorker
-
- PotentialMasterListWorker - Class in etomica.threaded.domain
-
- PotentialMasterListWorker(int, AtomTypeAgentManager, PotentialMasterListThreaded) - Constructor for class etomica.threaded.domain.PotentialMasterListWorker
-
- potentialMasterLong - Variable in class etomica.liquidLJ.LjMd3D
-
- potentialMasterLongCut - Variable in class etomica.liquidLJ.LjMd3D
-
- PotentialMasterLrc - Class in etomica.potential
-
Collects potentials used for long-range correction.
- PotentialMasterLrc() - Constructor for class etomica.potential.PotentialMasterLrc
-
- potentialMasterMonatomic - Variable in class etomica.normalmode.SimBennet
-
- potentialMasterMonatomic - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- potentialMasterMonatomic - Variable in class etomica.normalmode.SimTargetUmbrella
-
- potentialMasterMonatomic - Variable in class etomica.normalmode.SimUmbrella
-
- PotentialMasterMonatomic - Class in etomica.potential
-
PotentialMaster suitable for monatomic molecules without using neighbor
lists and avoids PotentialMaster's performance problems.
- PotentialMasterMonatomic(Simulation) - Constructor for class etomica.potential.PotentialMasterMonatomic
-
- PotentialMasterNbr - Class in etomica.nbr
-
- PotentialMasterNbr(Simulation, BoxAgentManager<? extends BoxCellManager>) - Constructor for class etomica.nbr.PotentialMasterNbr
-
- PotentialMasterNbrMolecular - Class in etomica.nbr.molecule
-
- PotentialMasterNbrMolecular(Simulation, BoxAgentManager.BoxAgentSource<? extends BoxCellManager>, BoxAgentManager<? extends BoxCellManager>) - Constructor for class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- potentialMasterRef - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- potentialMasterRef - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- PotentialMasterSite - Class in etomica.nbr.site
-
- PotentialMasterSite(Simulation, int, Space) - Constructor for class etomica.nbr.site.PotentialMasterSite
-
Invokes superclass constructor, specifying IteratorFactoryCell
for generating molecule iterators.
- PotentialMasterSite(Simulation, BoxAgentManager<BoxCellManager>, Space) - Constructor for class etomica.nbr.site.PotentialMasterSite
-
- PotentialMasterSite(Simulation, BoxAgentManager<? extends BoxCellManager>, AtomsetIteratorPDT) - Constructor for class etomica.nbr.site.PotentialMasterSite
-
- potentialMasterTarg - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- potentialMasterTarg - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- potentialMasterTarget - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- potentialMasterTarget - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- potentialMasterTarget - Variable in class etomica.normalmode.SimOverlap
-
- potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- potentialMasterTarget - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- potentialMCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- PotentialMEAM - Class in etomica.meam
-
- PotentialMEAM(Space) - Constructor for class etomica.meam.PotentialMEAM
-
- potentialMM - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potentialMM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialMM - Variable in class etomica.zeolite.ZeoliteSimulation
-
The hard-sphere potential governing the interactions.
- potentialMNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialMO - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- PotentialMolecular - Class in etomica.potential
-
Superclass for all Potential classes, which define how the atoms in the
system interact with each other.
- PotentialMolecular(int, Space) - Constructor for class etomica.potential.PotentialMolecular
-
General constructor for a potential instance
- potentialMolecularInterNonBondedUnlike - Variable in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- PotentialMolecularMonatomic - Class in etomica.potential
-
Intermolecular potential that wraps an atomic potential.
- PotentialMolecularMonatomic(Space, IPotentialAtomic) - Constructor for class etomica.potential.PotentialMolecularMonatomic
-
- PotentialMolecularSoft - Interface in etomica.potential
-
Methods for properties obtained for a soft, differentiable pair potential.
- PotentialMolecularSum - Class in etomica.potential
-
Molecular potential class that simply sums up contributions from multiple
(molecular) potentials.
- PotentialMolecularSum(IPotentialMolecular[]) - Constructor for class etomica.potential.PotentialMolecularSum
-
- potentialN - Variable in class etomica.meam.EFSTungsten
-
- potentialN - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- potentialN - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- potentialN - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- potentialN - Variable in class etomica.meam.MEAM_MC
-
- potentialN - Variable in class etomica.meam.MEAMMd3D
-
- PotentialN - Class in etomica.potential
-
- PotentialN(Space) - Constructor for class etomica.potential.PotentialN
-
Constructor for PotentialN.
- potentialN - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- potentialNN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialNN - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialNO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialNO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- PotentialNonAdditive - Class in etomica.virial
-
Potential class which computes non-additive energies from potentials
that return the full energies for various-sized groups of molecules.
- PotentialNonAdditive(IPotentialMolecular[]) - Constructor for class etomica.virial.PotentialNonAdditive
-
- PotentialNonAdditive(IPotentialMolecular[], int[]) - Constructor for class etomica.virial.PotentialNonAdditive
-
- PotentialNonAdditive.PotentialNonAdditiveNB - Class in etomica.virial
-
- PotentialNonAdditiveDifference - Class in etomica.potential
-
- PotentialNonAdditiveDifference(Space, IPotentialMolecular, IPotentialMolecular) - Constructor for class etomica.potential.PotentialNonAdditiveDifference
-
- PotentialNonAdditiveNB(int) - Constructor for class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
-
- potentialOHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialOHp - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialOO - Variable in class etomica.modules.catalysis.Catalysis
-
- potentialOO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- potentialOO - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- potentialOS - Variable in class etomica.modules.catalysis.Catalysis
-
- potentialPlus - Variable in class etomica.virial.MayerSphericalPlus
-
- PotentialPolarizable - Interface in etomica.potential
-
Interface for a polarizable potential.
- potentialQClCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQHCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQHNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQNaCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQNaNa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQOCl - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialQONa - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- PotentialReactive - Interface in etomica.potential
-
Interface for potentials that change the bond state of an atom.
- PotentialReactive.BondChangeData - Class in etomica.potential
-
- potentialRef - Variable in class etomica.virial.MayerPTAtt
-
- potentialRef - Variable in class etomica.virial.MayerSphericalPTAtt
-
- potentials - Variable in class etomica.virial.PotentialNonAdditive
-
- potentialsAndIterators - Variable in class etomica.chem.models.Model
-
- PotentialSoft - Interface in etomica.potential
-
Methods for properties obtained for a soft, differentiable pair potential.
- potentialSpecies - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- potentialSpecies - Variable in class etomica.kmc.SimKMCMEAMadatom
-
- potentialSW - Variable in class etomica.modules.insertion.InsertionGraphic
-
- potentialSW - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- potentialSW - Variable in class etomica.modules.swmd.SwmdGraphic
-
- potentialTether - Variable in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
-
- potentialTether - Variable in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
- potentialTether - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- potentialTether - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialThreaded - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- potentialThreaded - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- potentialThreaded - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- PotentialThreaded - Class in etomica.threaded
-
- PotentialThreaded(Space, IPotentialAtomic[]) - Constructor for class etomica.threaded.PotentialThreaded
-
- PotentialTruncated - Interface in etomica.potential
-
Interface for a potential that is artificially truncated, and thus which can
provide a zero-body potential that (approximately) corrects for the
truncation.
- potentialwall - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialwall1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialwallPorousA - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialwallPorousA1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialwallPorousB - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialwallPorousB1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- potentialWater - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- potentialWrapper - Variable in class etomica.modules.colloid.ColloidSim
-
- potentialWrapper - Variable in class etomica.modules.insertion.Insertion
-
- potentialWrapper - Variable in class etomica.modules.pistoncylinder.PistonCylinder
-
- potentialWrapper - Variable in class etomica.modules.swmd.Swmd
-
- potentot(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
-
- potentot(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- potparts(int, int, double, int, int, int[], int[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- potparts_old(int, int, double, int, int, int[], int[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- pots(double, double, double) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- pow - Variable in class etomica.data.DataPumpListenerPow
-
- pow - Variable in class etomica.data.DataPumpListenerPowStrict
-
- Pow - Class in etomica.graph.operations
-
- Pow() - Constructor for class etomica.graph.operations.Pow
-
- pow(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Power function.
- pow(int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Raise to a positive power.
- pow(int) - Method in class etomica.veos.bigdecimal.Ifactor
-
Exponentiation with a positive integer.
- pow(int) - Method in class etomica.veos.bigdecimal.Rational
-
Power to an integer.
- pow(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
Power to an integer.
- pow(Rational) - Method in class etomica.veos.bigdecimal.Rational
-
Raise to a rational power.
- pow - Variable in class etomica.virial.MCMoveClusterAtomChainHSTail
-
- Power - Class in etomica.units.dimensions
-
Dimension for all power units.
- power() - Method in class etomica.units.systems.CGS
-
- power() - Method in class etomica.units.systems.LJ
-
- power() - Method in class etomica.units.systems.MKS
-
- power() - Method in class etomica.units.systems.UnitSystem
-
- power() - Method in class etomica.units.systems.UnitSystem.Sim
-
- powerD(int) - Method in class etomica.space.Space
-
- powerD(double) - Method in class etomica.space.Space
-
- powerD(int) - Method in class etomica.space1d.Space1D
-
- powerD(double) - Method in class etomica.space1d.Space1D
-
- powerD(int) - Method in class etomica.space2d.Space2D
-
- powerD(double) - Method in class etomica.space2d.Space2D
-
- powerD(int) - Method in class etomica.space3d.Space3D
-
- powerD(double) - Method in class etomica.space3d.Space3D
-
- PowParameters - Class in etomica.graph.operations
-
- PowParameters(byte) - Constructor for class etomica.graph.operations.PowParameters
-
- powRound(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Raise to an integer power and round.
- powRound(BigDecimal, BigInteger) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Raise to an integer power and round.
- powRound(BigDecimal, Rational) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Raise to a fractional power and round.
- pPade - Variable in class etomica.math.numerical.VirialOptimizer
-
- PREC - Static variable in class etomica.math.Gamma
-
- prec2err(double, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Convert a precision (relative error) to an absolute error.
- precalcQ - Variable in class etomica.virial.ClusterSumHS
-
- precalcQ - Variable in class etomica.virial.ClusterWheatleyHS
-
- precalcQ - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- precision - Variable in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArray
-
- precision - Variable in class etomica.graphics.DeviceBox
-
Integer specifying the number of significant figures to be displayed.
- precision - Variable in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
- precision_s - Variable in class etomica.potential.EwaldSumMolecules
-
- precisionLimit - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
-
- precisionLimit - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- PreconditionedConjugateGradient - Class in etomica.conjugategradient
-
- PreconditionedConjugateGradient(Matrix, Matrix, Matrix, Matrix, int) - Constructor for class etomica.conjugategradient.PreconditionedConjugateGradient
-
- PreconditionedConjugateGradientAlgorithm() - Method in class etomica.conjugategradient.PreconditionedConjugateGradient
-
Preconditioned Conjugate Gradient solution for
Ax = b
- predefinedArgbs - Static variable in class org.jmol.util.Colix
-
- predefinedGroup1Names - Static variable in class org.jmol.viewer.JmolConstants
-
- predefinedGroup3Names - Static variable in class org.jmol.viewer.JmolConstants
-
- predefinedStatic - Static variable in class org.jmol.viewer.JmolConstants
-
- predefinedVariable - Static variable in class org.jmol.viewer.JmolConstants
-
- predictor() - Method in class etomica.integrator.IntegratorGear4
-
- predictor() - Method in class etomica.integrator.IntegratorGear4NPH
-
- Prefix - Enum in etomica.units
-
Base class for all unit prefixes, such as kilo, micro, nano, etc.
- prefix() - Method in class etomica.units.PrefixedUnit
-
- prefixAllowed() - Method in class etomica.units.CompoundUnit
-
- prefixAllowed() - Method in class etomica.units.PrefixedUnit
-
- prefixAllowed() - Method in class etomica.units.SimpleUnit
-
Some units (such as Angstroms) are not normally defined with a prefix
attached, and for such units this flag can be set to false to prohibit
the application of a prefix.
- prefixAllowed() - Method in class etomica.units.systems.LJ.LJUnit
-
- prefixAllowed() - Method in interface etomica.units.Unit
-
Indicates if the unit is appropriate for use with a prefix.
- PrefixedUnit - Class in etomica.units
-
Implementation of the Unit interface formed from a base Unit (e.
- PrefixedUnit(Unit) - Constructor for class etomica.units.PrefixedUnit
-
Constructs a PrefixedUnit using the given base and a Null prefix
- PrefixedUnit(Prefix, Unit) - Constructor for class etomica.units.PrefixedUnit
-
Constructs a PrefixedUnit using the given prefix and base.
- preMultiply(Quaternion) - Method in class etomica.math.Quaternion
-
Returns the Quaternion r resulting from multiplying the input Quaternion preMultiplier to the current Quaternion q.
- prepForGradient() - Method in class etomica.meam.P2EAM
-
- pRes - Variable in class etomica.normalmode.MeterSolidDA
-
- preservestate - Static variable in class org.jmol.script.Token
-
- press() - Method in class etomica.graphics.DeviceButton
-
Performs the button's action.
- press() - Method in class etomica.zeolite.DeviceButtonSingle
-
Performs the button's action.
- pressure - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
-
- pressure - Variable in class etomica.association.MCMoveVolumeAssociated
-
- pressure - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- pressure - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- pressure - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- pressure - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- pressure - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
-
- pressure - Variable in class etomica.data.meter.MeterWidomInsertion
-
- pressure - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
-
- pressure - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- pressure - Variable in class etomica.liquidLJ.MeterWidomInsertionP
-
- pressure - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- pressure - Variable in class etomica.models.nitrogen.MCMoveVolumeN2
-
- pressure - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
-
- pressure(double) - Method in class etomica.modules.adsorption.EOSSW
-
- pressure(double) - Method in class etomica.modules.adsorption.EOSSWPatel
-
- pressure - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- pressure(double) - Method in class etomica.modules.adsorption.VEOS3SW
-
- pressure - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
-
- pressure - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- pressure - Variable in class etomica.normalmode.MCMoveVolumeSolid
-
- pressure - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- pressure - Variable in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- pressure - Variable in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- pressure - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- pressure - Variable in class etomica.statmech.HardSphereSolid.EOSParams
-
- Pressure - Class in etomica.units.dimensions
-
Dimension for (3D) pressure.
- pressure() - Method in class etomica.units.systems.CGS
-
- pressure() - Method in class etomica.units.systems.LJ
-
- pressure() - Method in class etomica.units.systems.MKS
-
- pressure() - Method in class etomica.units.systems.UnitSystem
-
- pressure() - Method in class etomica.units.systems.UnitSystem.Sim
-
- pressure - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- pressure0 - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- Pressure2D - Class in etomica.units.dimensions
-
Simulation unit of (2D) pressure is (D-A/ps^2)/A = D/ps^2
- pressure2D() - Method in class etomica.units.systems.UnitSystem.Sim
-
- pressureAverage - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- pressureDisplayTextBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pressureFast - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- pressureFull - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- pressureHistory - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- pressureMeter - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pressurePump - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- pressureSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pressureSliderPanel - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pressureTensor - Variable in class etomica.dimer.PotentialCalculationForcePressureSumGB
-
- pressureTensor - Variable in class etomica.integrator.IntegratorRigidIterative
-
- pressureTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- pressureTensor - Variable in class etomica.integrator.IntegratorVelocityVerlet
-
- pressureTensor - Variable in class etomica.integrator.IntegratorVerlet
-
- pressureTensor - Variable in class etomica.modules.droplet.IntegratorDroplet
-
- pressureTensor - Variable in class etomica.potential.PotentialCalculationForcePressureSum
-
- pressureTensor - Variable in class etomica.potential.PotentialCalculationPressureTensor
-
- pressureTensor - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- pretendBox - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- pretendBox - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- pretendBox - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- pretendBox - Variable in class etomica.normalmode.MeterDDP
-
- pretendBox - Variable in class etomica.normalmode.MeterDP
-
- pretendBox - Variable in class etomica.normalmode.MeterTargetTP
-
- prev - Variable in class etomica.lattice.IndexIteratorIncreasing
-
- prev - Static variable in class org.jmol.script.Token
-
- previous - Variable in class etomica.math.function.FunctionChain.Link
-
- previous - Variable in class etomica.util.TreeLinker
-
- previousTensor - Variable in class etomica.models.water.OrientationCalcWater3P
-
- previousTensor - Variable in class etomica.models.water.OrientationCalcWater4P
-
- previousValue - Variable in class etomica.normalmode.ModifierCells3D
-
- previousValue - Variable in class etomica.normalmode.ModifierXCells2D
-
- previousValue - Variable in class etomica.normalmode.ModifierYCells2D
-
- prevprime(BigInteger) - Method in class etomica.veos.bigdecimal.Prime
-
return the largest prime smaller than n
- pRigid - Variable in class etomica.potential.P2WaterPotentialsJankowski
-
- primaryCoordDef - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- primaryCoordDef - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- Prime - Class in etomica.veos.bigdecimal
-
Prime numbers.
- Prime() - Constructor for class etomica.veos.bigdecimal.Prime
-
Default constructor initializing a list of primes up to 17.
- primeexp - Variable in class etomica.veos.bigdecimal.Ifactor
-
- primitive - Variable in class etomica.lattice.BravaisLattice
-
- Primitive - Class in etomica.lattice.crystal
-
Collection of primitive elements that specify or are determined
by the structure of a Bravais lattice.
- Primitive(Space) - Constructor for class etomica.lattice.crystal.Primitive
-
This constructor is called directly when a Primitive is constructing
its reciprocal primitive.
- primitive - Variable in class etomica.models.hexane.SimHarmonicHexane
-
- primitive - Variable in class etomica.models.hexane.TestHexane
-
- primitive - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- primitive - Variable in class etomica.models.hexane.TestHexaneHarmonic
-
- primitive - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- primitive - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- primitive - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- primitive - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- primitive - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- primitive - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- primitive - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- primitive - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImage
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- primitive - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- primitive - Variable in class etomica.models.oneDHardRods.SimExtensiveTest
-
- primitive - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- primitive - Variable in class etomica.models.oneDHardRods.SimWidomMode
-
- primitive - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- primitive - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- primitive - Variable in class etomica.normalmode.CoordinateDefinition
-
- primitive - Variable in class etomica.normalmode.HessianDB
-
- primitive - Variable in class etomica.normalmode.LJVacancyMin
-
- primitive - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- primitive - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- primitive - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- primitive - Variable in class etomica.normalmode.NormalModes2D
-
- primitive - Variable in class etomica.normalmode.NormalModes3D
-
- primitive - Variable in class etomica.normalmode.NormalModesMolecular
-
- primitive - Variable in class etomica.normalmode.SimBennet
-
- primitive - Variable in class etomica.normalmode.SimCalcJ
-
- primitive - Variable in class etomica.normalmode.SimCalcS
-
- primitive - Variable in class etomica.normalmode.SimCalcSLJ
-
- primitive - Variable in class etomica.normalmode.SimCalcSMorse
-
- primitive - Variable in class etomica.normalmode.SimCalcSSoftSphere2D
-
- primitive - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- primitive - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- primitive - Variable in class etomica.normalmode.SimEinStep1
-
- primitive - Variable in class etomica.normalmode.SimEinStep1HCP
-
- primitive - Variable in class etomica.normalmode.SimEinStep2
-
- primitive - Variable in class etomica.normalmode.SimEinStep2HCP
-
- primitive - Variable in class etomica.normalmode.SimHarmonic
-
- primitive - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- primitive - Variable in class etomica.normalmode.SimLJHTTISuper
-
- primitive - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- primitive - Variable in class etomica.normalmode.SimModesJ
-
- primitive - Variable in class etomica.normalmode.SimOverlap
-
- primitive - Variable in class etomica.normalmode.SimOverlapLJ
-
- primitive - Variable in class etomica.normalmode.SimOverlapLJModule
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereDP
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereEin
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereTP
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- primitive - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- primitive - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- primitive - Variable in class etomica.normalmode.SimTarget
-
- primitive - Variable in class etomica.normalmode.SimTargetUmbrella
-
- primitive - Variable in class etomica.normalmode.SimUmbrella
-
- primitive - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- primitive - Variable in class etomica.normalmode.WaveVectorFactory2D
-
- primitive - Variable in class etomica.normalmode.WaveVectorFactoryFcc
-
- primitive - Variable in class etomica.normalmode.WaveVectorFactorySimple
-
- primitive - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- primitive - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- primitive - Variable in class etomica.paracetamol.SimulationOrthorhombicParacetamol
-
- PrimitiveBcc - Class in etomica.lattice.crystal
-
Primitive group for a body-centered-cubic system.
- PrimitiveBcc(Space) - Constructor for class etomica.lattice.crystal.PrimitiveBcc
-
- PrimitiveBcc(Space, double) - Constructor for class etomica.lattice.crystal.PrimitiveBcc
-
- PrimitiveCubic - Class in etomica.lattice.crystal
-
Primitive group for a cubic system.
- PrimitiveCubic(Space) - Constructor for class etomica.lattice.crystal.PrimitiveCubic
-
- PrimitiveCubic(Space, double) - Constructor for class etomica.lattice.crystal.PrimitiveCubic
-
- PrimitiveFcc - Class in etomica.lattice.crystal
-
Primitive group for a face-centered-cubic system.
- PrimitiveFcc(Space) - Constructor for class etomica.lattice.crystal.PrimitiveFcc
-
- PrimitiveFcc(Space, double) - Constructor for class etomica.lattice.crystal.PrimitiveFcc
-
- PrimitiveGeneral - Class in etomica.lattice.crystal
-
Primitive defined simply by its vectors.
- PrimitiveGeneral(Space, Vector[]) - Constructor for class etomica.lattice.crystal.PrimitiveGeneral
-
- PrimitiveHCP4 - Class in etomica.lattice.crystal
-
Orthorhombic primitive cell for an HCP system.
- PrimitiveHCP4(Space) - Constructor for class etomica.lattice.crystal.PrimitiveHCP4
-
- PrimitiveHCP4(Space, double) - Constructor for class etomica.lattice.crystal.PrimitiveHCP4
-
- PrimitiveHexagonal - Class in etomica.lattice.crystal
-
Primitive group for a hexagonal system.
- PrimitiveHexagonal(Space) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal
-
- PrimitiveHexagonal(Space, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal
-
- PrimitiveHexagonal.PrimitiveHexagonalReciprocal - Class in etomica.lattice.crystal
-
- PrimitiveHexagonal2D - Class in etomica.lattice.crystal
-
Primitive group for a 2D hexagonal system.
- PrimitiveHexagonal2D(Space) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- PrimitiveHexagonal2D(Space, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal - Class in etomica.lattice.crystal
-
- PrimitiveHexagonal2DReciprocal(Space, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal
-
- PrimitiveHexagonalReciprocal(Space, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveHexagonal.PrimitiveHexagonalReciprocal
-
- PrimitiveHexane - Class in etomica.models.hexane
-
Implements the triclinic crystal structure derived from Dr.
- PrimitiveHexane(Space) - Constructor for class etomica.models.hexane.PrimitiveHexane
-
- PrimitiveMonoclinic - Class in etomica.lattice.crystal
-
Primitive group for a monoclinic system.
- PrimitiveMonoclinic(Space) - Constructor for class etomica.lattice.crystal.PrimitiveMonoclinic
-
- PrimitiveMonoclinic(Space, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveMonoclinic
-
- PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal - Class in etomica.lattice.crystal
-
- PrimitiveMonoclinicReciprocal(Space, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal
-
- PrimitiveOrthorhombic - Class in etomica.lattice.crystal
-
Primitive group for an orthorhombic system.
- PrimitiveOrthorhombic(Space) - Constructor for class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- PrimitiveOrthorhombic(Space, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- PrimitiveOrthorhombicHexagonal - Class in etomica.lattice.crystal
-
Primitive group for an orthorhombic system.
- PrimitiveOrthorhombicHexagonal(Space, double) - Constructor for class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
- PrimitiveTetragonal - Class in etomica.lattice.crystal
-
Primitive group for a tetragonal system.
- PrimitiveTetragonal(Space) - Constructor for class etomica.lattice.crystal.PrimitiveTetragonal
-
- PrimitiveTetragonal(Space, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveTetragonal
-
- PrimitiveTriclinic - Class in etomica.lattice.crystal
-
Primitive group for a triclinic system.
- PrimitiveTriclinic(Space) - Constructor for class etomica.lattice.crystal.PrimitiveTriclinic
-
- PrimitiveTriclinic(Space, double, double, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveTriclinic
-
- PrimitiveTrigonal - Class in etomica.lattice.crystal
-
Primitive group for a trigonal system.
- PrimitiveTrigonal(Space) - Constructor for class etomica.lattice.crystal.PrimitiveTrigonal
-
- PrimitiveTrigonal(Space, double, double, double, double) - Constructor for class etomica.lattice.crystal.PrimitiveTrigonal
-
- primitiveUnitCell - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- primitiveUnitCell - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- primitiveUnitCell - Variable in class etomica.normalmode.HessianDB
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimCalcSLJ
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimCalcSSoftSphereFCC
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapLJ
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- primitiveUnitCell - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- print(Parser.CommandVariable) - Method in class etomica.graph.engine.Interpreter
-
- print - Variable in class etomica.potential.P2HydrogenHindePatkowski
-
- print - Variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- print - Variable in class etomica.potential.P2HydrogenPatkowski
-
- print - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- print() - Method in class etomica.virial.ClusterWheatleyPartitionScreening.FrequencyCounter
-
- printapalooza - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- printInConvertedUnits - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- printInterval - Variable in class etomica.integrator.IntegratorRigidIterative
-
- printInterval - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- printInterval - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- printInterval - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- printKeyAtomPositions() - Method in class etomica.action.IntegratorDimerApproach
-
- printResults(double) - Method in class etomica.virial.simulations.SimulationVirial
-
- printResults(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- printResults(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- printResults(double, String[]) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- printStrands(List, int) - Static method in class etomica.graph.property.FFTDecomposition
-
- printStrands(List, int) - Static method in class etomica.graph.property.IsFFT
-
- printStrands(List, int) - Static method in class etomica.virial.CalcFFT
-
- printTargetHistogram() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
Prints out the target histogram of maximum separation distances as
set up by setupTargetHistogram().
- probabilityBins - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- probabilityBins - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- probabilityReverseMap - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- probabilityReverseMap - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- probe - Static variable in class org.jmol.script.Token
-
- proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) - Method in class etomica.graph.view.rasterizer.DefaultSVGConverterController
-
Invoked when the rasterizer got an error while
transcoding the input source.
- proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) - Method in class etomica.graph.view.rasterizer.Main
-
- proceedOnSourceTranscodingFailure(SVGConverterSource, File, String) - Method in interface etomica.graph.view.rasterizer.SVGConverterController
-
Invoked when the rasterizer got an error while
transcoding the input source.
- proceedWithComputedTask(Transcoder, Map, List, List) - Method in class etomica.graph.view.rasterizer.DefaultSVGConverterController
-
Invoked when the rasterizer has computed the
exact description of what it should do.
- proceedWithComputedTask(Transcoder, Map, List, List) - Method in class etomica.graph.view.rasterizer.Main
-
- proceedWithComputedTask(Transcoder, Map, List, List) - Method in interface etomica.graph.view.rasterizer.SVGConverterController
-
Invoked when the rasterizer has computed the
exact description of what it should do.
- proceedWithSourceTranscoding(SVGConverterSource, File) - Method in class etomica.graph.view.rasterizer.DefaultSVGConverterController
-
Invoked when the rasterizer is about to start transcoding
of a given source.
- proceedWithSourceTranscoding(SVGConverterSource, File) - Method in class etomica.graph.view.rasterizer.Main
-
- proceedWithSourceTranscoding(SVGConverterSource, File) - Method in interface etomica.graph.view.rasterizer.SVGConverterController
-
Invoked when the rasterizer is about to start transcoding
of a given source.
- processAtoms(IAtomList) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- processData(IData) - Method in class etomica.data.AccumulatorAverageBootstrap
-
- processData(IData) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- processData(IData) - Method in class etomica.data.DataAccumulator
-
Returns getData() every pushInterval times it is invoked, otherwise returns null
(thereby preventing transmission of data to the next DataSinks).
- processData(IData) - Method in class etomica.data.DataGroupFilter
-
Returns the output data that was established with a previous call to
processDataInfo.
- processData(IData) - Method in class etomica.data.DataLogger
-
Gives data to DataSink for writing
- processData(IData) - Method in class etomica.data.DataProcessor
-
Processes the input Data and returns Data for pushing to the next
DataSink.
- processData(IData) - Method in class etomica.data.DataProcessorChemicalPotential
-
- processData(IData) - Method in class etomica.data.DataProcessorFunction
-
Applies the function to all elements of the input data.
- processData(IData) - Method in class etomica.data.DataProcessorInterfacialTension
-
- processData(IData) - Method in class etomica.data.DataPump
-
Returns the given Data.
- processData(IData) - Method in class etomica.data.types.CastGroupOfTablesToDataTable
-
Converts data in given group to a DataDoubleArray as described in the
general comments for this class.
- processData(IData) - Method in class etomica.data.types.CastGroupToDoubleArray
-
Converts data in given group to a DataDoubleArray as described in the
general comments for this class.
- processData(IData) - Method in class etomica.data.types.CastToDouble
-
Extracts a double from the input data and returns it encapsulated in a
DataDouble.
- processData(IData) - Method in class etomica.data.types.CastToDoubleArray
-
Copies input Data to a DataDoubleArray and returns it (the DataDataDoubleArray).
- processData(IData) - Method in class etomica.data.types.CastToGroup
-
Processes the input Data to update the output DataGroup.
- processData(IData) - Method in class etomica.data.types.CastToTable
-
Copies input Data to a DataTable and returns it (the DataTable).
- processData(IData) - Method in class etomica.densityofstate.DataProcessorPhi
-
- processData(IData) - Method in class etomica.liquidLJ.DataProcessorReweight
-
- processData(IData) - Method in class etomica.liquidLJ.DataProcessorReweightRatio
-
- processData(IData) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
-
- processData(IData) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- processData(IData) - Method in class etomica.meam.DataProcessorCvMD
-
- processData(IData) - Method in class etomica.metastable.DataProcessorXY
-
- processData(IData) - Method in class etomica.models.hexane.TestHexaneHarmonic.DataProcessorFoo
-
- processData(IData) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg
-
- processData(IData) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg2
-
- processData(IData) - Method in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
-
- processData(IData) - Method in class etomica.modules.entropylottery.EntropyProcessor
-
- processData(IData) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- processData(IData) - Method in class etomica.modules.interfacial.FitTanh
-
- processData(IData) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
-
- processData(IData) - Method in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
-
- processData(IData) - Method in class etomica.modules.mu.MuGraphic.DataProcessorMu
-
- processData(IData) - Method in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
-
- processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorBias
-
- processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
-
- processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- processData(IData) - Method in class etomica.modules.multiharmonic.DataProcessorVar
-
- processData(IData) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
-
- processData(IData) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
-
- processData(IData) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
-
- processData(IData) - Method in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
-
- processData(IData) - Method in class etomica.modules.statistics.AccumulatorMimicMu
-
- processData(IData) - Method in class etomica.modules.statistics.DataProcessorBounds
-
- processData(IData) - Method in class etomica.modules.statistics.DataProcessorMu
-
- processData(IData) - Method in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- processData(IData) - Method in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
-
- processData(IData) - Method in class etomica.normalmode.BoltzmannProcessor
-
- processData(IData) - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
-
- processData(IData) - Method in class etomica.normalmode.DataProcessorSum
-
- processData(IData) - Method in class etomica.surfacetension.DataProcessorSurfaceTension
-
- processData(IData) - Method in class etomica.surfacetension.FitTanh
-
- processData(IData) - Method in class etomica.surfacetension.SurfaceTensionMapped
-
- processData(IData) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
take in v1/pi1, pi0/pi1, spit out v1/pi, overlap0, overlap1, overlap2...
- processData(IData) - Method in class etomica.virial.simulations.VirialPolyhedra.DataProcessorR2
-
- processData(IData) - Method in class etomica.virial.simulations.VirialPolyhedra2.DataProcessorR2
-
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorAverage
-
Prepares the accumulator for input data.
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorAverageBlockless
-
Prepares the accumulator for input data.
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorAverageBootstrap
-
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorAverageCollapsing
-
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorAverageCovariance
-
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorAverageFixed
-
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorAverageFixedOutputFile
-
Prepares the accumulator for input data.
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorCounter
-
Does nothing.
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorHistogram
-
Sets up data and histograms, discarding any previous results.
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorHistory
-
Sets up data and histories, discarding any previous results.
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorRatioAverageCovariance
-
- processDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- processDataInfo(IDataInfo) - Method in class etomica.data.DataGroupFilter
-
Determines data that will be output, using the given DataInfo and
the index specification given at construction.
- processDataInfo(IDataInfo) - Method in class etomica.data.DataLogger
-
- processDataInfo(IDataInfo) - Method in class etomica.data.DataProcessor
-
Informs this DataProcessor of the DataInfo for the Data it will be
processing.
- processDataInfo(IDataInfo) - Method in class etomica.data.DataProcessorChemicalPotential
-
- processDataInfo(IDataInfo) - Method in class etomica.data.DataProcessorFunction
-
Returns a copy of the given dataInfo
- processDataInfo(IDataInfo) - Method in class etomica.data.DataProcessorInterfacialTension
-
- processDataInfo(IDataInfo) - Method in class etomica.data.DataPump
-
Returns the given DataInfo.
- processDataInfo(IDataInfo) - Method in class etomica.data.types.CastGroupOfTablesToDataTable
-
Prepares processor to handle Data.
- processDataInfo(IDataInfo) - Method in class etomica.data.types.CastGroupToDoubleArray
-
Prepares processor to handle Data.
- processDataInfo(IDataInfo) - Method in class etomica.data.types.CastToDouble
-
Prepares processor to handle Data.
- processDataInfo(IDataInfo) - Method in class etomica.data.types.CastToDoubleArray
-
Prepares processor to perform cast.
- processDataInfo(IDataInfo) - Method in class etomica.data.types.CastToGroup
-
- processDataInfo(IDataInfo) - Method in class etomica.data.types.CastToTable
-
Prepares processor to perform cast.
- processDataInfo(IDataInfo) - Method in class etomica.densityofstate.DataProcessorPhi
-
- processDataInfo(IDataInfo) - Method in class etomica.liquidLJ.DataProcessorReweight
-
- processDataInfo(IDataInfo) - Method in class etomica.liquidLJ.DataProcessorReweightRatio
-
- processDataInfo(IDataInfo) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorCorrection
-
- processDataInfo(IDataInfo) - Method in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- processDataInfo(IDataInfo) - Method in class etomica.meam.DataProcessorCvMD
-
- processDataInfo(IDataInfo) - Method in class etomica.metastable.DataProcessorXY
-
- processDataInfo(IDataInfo) - Method in class etomica.models.hexane.TestHexaneHarmonic.DataProcessorFoo
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.chainequilibrium.MolecularWeightAvg2
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.droplet.DropletGraphic.DataProcessorTensorSplitter
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.entropylottery.EntropyProcessor
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.interfacial.FitTanh
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.DataProcessorTensorSplitter
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.ljmd.LjmdGraphic.DataProcessorTensorTrace
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataProcessorMu
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.mu.MuGraphic.DataSinkExcludeOverlap
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBias
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorDyDLnx
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.multiharmonic.DataProcessorVar
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataProcessAHT
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.DataSinkExcludeOverlap
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.statistics.DataProcessorBounds
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.statistics.DataProcessorMu
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- processDataInfo(IDataInfo) - Method in class etomica.modules.swmd.SwmdGraphic.DataSinkExcludeOverlap
-
- processDataInfo(IDataInfo) - Method in class etomica.normalmode.BoltzmannProcessor
-
- processDataInfo(IDataInfo) - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
-
- processDataInfo(IDataInfo) - Method in class etomica.normalmode.DataProcessorSum
-
- processDataInfo(IDataInfo) - Method in class etomica.surfacetension.DataProcessorSurfaceTension
-
- processDataInfo(IDataInfo) - Method in class etomica.surfacetension.FitTanh
-
- processDataInfo(IDataInfo) - Method in class etomica.surfacetension.SurfaceTensionMapped
-
- processDataInfo(IDataInfo) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- processDataInfo(IDataInfo) - Method in class etomica.virial.simulations.VirialPolyhedra.DataProcessorR2
-
- processDataInfo(IDataInfo) - Method in class etomica.virial.simulations.VirialPolyhedra2.DataProcessorR2
-
- processReverseList() - Method in class etomica.integrator.IntegratorHard
-
Recalculate collision times (up) for any atoms atoms in the "reverse"
list of atoms that thought they would collide with an atom that's
changed.
- product(ClusterDiagram, ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations
-
Returns a new cluster that is the product of the given clusters.
- product(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Returns the product of all the given clusters.
- product(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Returns an array of clusters formed from taking the product of each of the diagrams
of the first set with each of the diagrams of the second set.
- product(int[]) - Static method in class etomica.virial.cluster.Standard
-
Prepares a set of bond pairs for a clusters
formed from a disconnected set of fully connected subclusters.
- product3D(Vector, Vector, Vector) - Method in class etomica.potential.P2SpheroPolyhedron
-
- profile1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- profile1pump - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- profile2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- profile2pump - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- profileData - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- profileDataInfo - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- profileDim - Variable in class etomica.data.meter.MeterProfile
-
Vector describing the orientation of the profile.
- profileDim - Variable in class etomica.data.meter.MeterProfileByAtoms
-
Vector describing the orientation of the profile.
- profileDim - Variable in class etomica.data.meter.MeterProfileByVolume
-
Vector describing the orientation of the profile.
- profileDim - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- profilePlot - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- proj - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- proja - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- projb - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- projectOntoAxis(Point3f, Point3f, Vector3f, Vector3f) - Static method in class org.jmol.util.Measure
-
- prompt(String, String, String[], boolean) - Method in interface org.jmol.api.ApiPlatform
-
- prompt(String, String, String[], boolean) - Method in class org.jmol.awt.Platform
-
- prop - Variable in class etomica.graph.operations.MaxIsomorph.MaxIsomorphParameters
-
- PropertiesResource - Class in etomica.server.resources
-
- PropertiesResource(SimulationStore) - Constructor for class etomica.server.resources.PropertiesResource
-
- property - Variable in class etomica.graph.operations.SetPropertyFilter
-
- Property - Interface in etomica.graph.property
-
- property - Variable in class etomica.graphics.DeviceSlider
-
Property being modulated
- property - Variable in class etomica.graphics.DeviceSpinner
-
Property being modulated
- Property - Interface in etomica.meta.properties
-
Created by kofke on 7/23/17.
- property - Variable in class etomica.modifier.ModifierGeneral
-
- property - Variable in class etomica.server.representations.PropertyUpdate
-
- property - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- property - Variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- property - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- property - Static variable in class org.jmol.script.Token
-
- PROPERTY_ALL - Static variable in class etomica.graph.operations.MaxIsomorph
-
- propertyatomnumbercolumncount - Static variable in class org.jmol.script.Token
-
- propertyatomnumberfield - Static variable in class org.jmol.script.Token
-
- propertyChange(PropertyChangeEvent) - Method in class etomica.graphics.PropertyText
-
Listen to update display if editor changes value in some other way.
- propertyChange(PropertyChangeEvent) - Method in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
Called when a field's "value" property changes.
- propertycolorscheme - Static variable in class org.jmol.script.Token
-
- propertydatacolumncount - Static variable in class org.jmol.script.Token
-
- propertydatafield - Static variable in class org.jmol.script.Token
-
- PropertyFilter - Class in etomica.graph.iterators.filters
-
- PropertyFilter(GraphIterator, Property) - Constructor for class etomica.graph.iterators.filters.PropertyFilter
-
- propertyFilter - Variable in class etomica.graph.operations.AllIsomorphs.AllIsomorphsParameters
-
- PROPERTYFLAGS - Static variable in class org.jmol.script.Token
-
- PropertyImpl - Class in etomica.graph.engine.impl
-
- PropertyImpl(String) - Constructor for class etomica.graph.engine.impl.PropertyImpl
-
- PropertySerializer - Class in etomica.server.serializers
-
- PropertySerializer(Class<Property>) - Constructor for class etomica.server.serializers.PropertySerializer
-
- PropertyText - Class in etomica.graphics
-
- PropertyText(PropertyEditor) - Constructor for class etomica.graphics.PropertyText
-
- PropertyUpdate - Class in etomica.server.representations
-
- PropertyUpdate() - Constructor for class etomica.server.representations.PropertyUpdate
-
- PropertyUpdate(long, String, Object) - Constructor for class etomica.server.representations.PropertyUpdate
-
- pRotConstraint - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- PRotConstraint - Class in etomica.models.nitrogen
-
- PRotConstraint(Space, CoordinateDefinitionNitrogen, Box) - Constructor for class etomica.models.nitrogen.PRotConstraint
-
- pRotConstraint - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- pRotConstraint - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- pRotConstraint - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- protein - Static variable in class org.jmol.script.Token
-
- Psat - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- pSat() - Method in class etomica.modules.adsorption.EOSSW
-
- psi(double) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Digamma function.
- psi - Static variable in class org.jmol.script.Token
-
- pSimData - Variable in class etomica.math.numerical.VirialOptimizer
-
- pSoluteMM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- pSolutePM - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- pSolutePP - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- pSpan - Variable in class etomica.normalmode.MeterDDP
-
- pSpan - Variable in class etomica.normalmode.MeterDP
-
- pSpan - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- pSplitter - Variable in class etomica.normalmode.DataSourceAvgPressure
-
- pSplitter - Variable in class etomica.normalmode.DataSourceAvgPressure2
-
- pSplitter - Variable in class etomica.normalmode.DataSourceMuRoot
-
- pSplitter - Variable in class etomica.normalmode.DataSourceMuRoot1
-
- pSplitter - Variable in class etomica.normalmode.DataSourceMuRootPMatch
-
- pSplitter - Variable in class etomica.normalmode.DataSourcePMu
-
- pSplitter - Variable in class etomica.normalmode.DataSourcePN
-
- psuedoSinks - Variable in class etomica.data.DataSet
-
- pSum - Variable in class etomica.normalmode.HSNPT.MyAgent
-
- pSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- pSum2 - Variable in class etomica.normalmode.HSNPT.MyAgent
-
- pSumXYZ - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- pSumXYZ1 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
-
- pSumXYZ1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- pSumXYZ2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
-
- pSumXYZ2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- pt - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- pt - Variable in enum org.jmol.constant.EnumVdw
-
- pt4Value(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- pThermalize - Variable in class etomica.modules.adsorption.P1Wall
-
- pTmp - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- pTmp1 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- pTmp1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- pTmp2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- pTmp2 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- pTruncated - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- pTruncatedAA - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- pTruncatedAB - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- ptValue(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- pTW - Variable in class etomica.interfacial.LJMC
-
- pTW - Variable in class etomica.interfacial.LJMD
-
- pType - Variable in class etomica.models.nitrogen.SpeciesN2
-
- pType - Variable in class etomica.models.nitrogen.SpeciesN2B
-
- pType - Variable in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- pU - Variable in class etomica.virial.MayerENonGeneral
-
- pullFactor - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- pump - Variable in class etomica.simulation.prototypes.LJMD3D
-
- pump - Variable in class etomica.spin.Heisenberg
-
- pump - Variable in class etomica.thermointegration.LjMc3D
-
- pumpRG - Variable in class etomica.simulation.prototypes.ChainHSMD3D
-
- pUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- pUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- pUnit - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- pUnit - Variable in class etomica.modules.swmd.SwmdGraphic
-
- purine - Static variable in class org.jmol.script.Token
-
- PURPLE - Static variable in class org.jmol.util.Colix
-
- pushHistograms() - Method in class etomica.data.AccumulatorAverageBootstrap
-
Constructs and pushes histograms to any histogram data sink.
- pushInterval - Variable in class etomica.data.DataAccumulator
-
Accumulated data are pushed to the data sinks after every pushInterval calls
- pushme - Static variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- pushme - Static variable in class etomica.virial.ClusterWheatleySoft
-
- pushme - Static variable in class etomica.virial.ClusterWheatleySoftBD
-
- pushme - Static variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- pushme - Static variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- pushmeval - Static variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- pushmeval - Static variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- pushR2 - Variable in class etomica.virial.ClusterSumMultibody
-
- pushR2 - Variable in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- pushR2 - Variable in class etomica.virial.ClusterSumPolarizable
-
- pushR2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- pushR2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- pushR2 - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- put(Integer, V) - Method in class etomica.util.collections.IndexMap
-
- put(int, V) - Method in class etomica.util.collections.IndexMap
-
- put(int, int) - Method in class org.jmol.util.Int2IntHash
-
- put_rigid() - Method in class etomica.potential.P2WaterPotentialsJankowski
-
- putAll(Map<? extends Integer, ? extends V>) - Method in class etomica.util.collections.IndexMap
-
- putCount - Variable in class etomica.data.DataAccumulator
-
Counter that keeps track of the number of interval events
received since last call to updateSums
- putData(IData) - Method in class etomica.data.DataArrayWriter
-
- putData(IData) - Method in class etomica.data.DataDistributer
-
- putData(IData) - Method in class etomica.data.DataDump
-
- putData(IData) - Method in class etomica.data.DataFork
-
Puts the given Data through into all DataSinks.
- putData(IData) - Method in class etomica.data.DataGroupSplitter
-
- putData(IData) - Method in class etomica.data.DataLogger
-
Performs the open/write/close file actions in accordance with the
settings of the Logger.
- putData(IData) - Method in class etomica.data.DataProcessor
-
Processes input Data and pushes it downstream if output Data and DataSink
are not null.
- putData(IData) - Method in class etomica.data.DataSet.DataSetSink
-
- putData(IData) - Method in class etomica.data.DataSinkConsole
-
Causes the given values to be written to the print stream.
- putData(IData) - Method in class etomica.data.DataSplitter
-
- putData(IData) - Method in class etomica.data.DataTableWriter
-
- putData(IData) - Method in interface etomica.data.IDataSink
-
Gives data to DataSink for processing, display, or whatever it does.
- putData(IData) - Method in class etomica.graphics.DisplayTextBox
-
Sets the display text to reflect the desired value from the datasource.
- putData(IData) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- putData(IData) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
Add the given values to the sums and block sums
- putData(IData) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- putData(IData) - Method in class etomica.modules.statistics.DataAccCorrectedPusher
-
- putData(IData) - Method in class etomica.modules.statistics.DataAccDiffCorrectedPusher
-
- putData(IData) - Method in class etomica.modules.statistics.DataAccDifficultyPusher
-
- putData(IData) - Method in class etomica.modules.statistics.DataAccPusher
-
- putData(IData) - Method in class etomica.modules.statistics.DataAccSamplesPusher
-
- putDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
Prepares the accumulator for input data.
- putDataInfo(IDataInfo) - Method in class etomica.data.AccumulatorAverageFixed
-
- putDataInfo(IDataInfo) - Method in class etomica.data.DataArrayWriter
-
- putDataInfo(IDataInfo) - Method in class etomica.data.DataDistributer
-
- putDataInfo(IDataInfo) - Method in class etomica.data.DataDump
-
- putDataInfo(IDataInfo) - Method in class etomica.data.DataFork
-
Puts the given DataInfo through into all DataSinks, inserting
a data caster before any sinks needing one.
- putDataInfo(IDataInfo) - Method in class etomica.data.DataGroupSplitter
-
- putDataInfo(IDataInfo) - Method in class etomica.data.DataProcessor
-
Invokes processDataInfo on the given DataInfo, and passes the returned
DataInfo to the dataSink (if not null).
- putDataInfo(IDataInfo) - Method in class etomica.data.DataSet.DataSetSink
-
- putDataInfo(IDataInfo) - Method in class etomica.data.DataSinkConsole
-
Causes the given DataInfo to be written to the print stream.
- putDataInfo(IDataInfo) - Method in class etomica.data.DataSplitter
-
- putDataInfo(IDataInfo) - Method in class etomica.data.DataTableWriter
-
- putDataInfo(IDataInfo) - Method in interface etomica.data.IDataSink
-
Informs the DataSink of the type of Data it should expect to receive.
- putDataInfo(IDataInfo) - Method in class etomica.graphics.DisplayTextBox
-
- putDataInfo(IDataInfo) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- putDataInfo(IDataInfo) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- putDataInfo(IDataInfo) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- putDataInfo(IDataInfo) - Method in class etomica.modules.statistics.AccumulatorMimicMu
-
- putDataInfo(IDataInfo) - Method in class etomica.modules.statistics.DataAccPusher
-
- putDataInfoInternal(IDataInfo) - Method in class etomica.data.DataArrayWriter
-
- putDataInfoInternal(IDataInfo) - Method in class etomica.data.DataTableWriter
-
- putDataInternal(IData) - Method in class etomica.data.DataArrayWriter
-
- putDataInternal(IData) - Method in class etomica.data.DataTableWriter
-
- putEdge(byte) - Method in interface etomica.graph.model.Graph
-
- putEdge(byte, byte) - Method in interface etomica.graph.model.Graph
-
- putEdge(byte, byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- putEdge(byte) - Method in class etomica.graph.model.impl.GraphImpl
-
- putValue(String, Object) - Method in class etomica.util.Grabber.ActionCornerSetter
-
- pvBox - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- pWater - Variable in class etomica.dielectric.TIP4P_NVT
-
- pWell - Variable in class etomica.virial.MCMoveClusterAtomSQWChain
-
- pWell - Variable in class etomica.virial.MCMoveClusterAtomSQWTree
-
- pWertheim2Site - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- Pwr2 - Static variable in class org.jmol.util.TriangleData
-
- PY - Static variable in class etomica.virial.cluster.ClusterOperations
-
- PYGenerate(int, char) - Static method in class etomica.virial.PYGenerator
-
Returns the graphs (at each order, up to n+2) in the PY approximation to c.
- PYGenerator - Class in etomica.virial
-
- PYGenerator() - Constructor for class etomica.virial.PYGenerator
-
- PYGenerator.IteratorEF - Class in etomica.virial
-
- pyrimidine - Static variable in class org.jmol.script.Token
-
Q
- Q - Variable in class etomica.conjugategradient.ConjugateGradients
-
- Q - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- Q - Variable in class etomica.conjugategradient.SteepestDescent
-
- q(double, double, double) - Static method in class etomica.freeenergy.npath.SimLattice
-
- q - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- q - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- q - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- q - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- q - Variable in class etomica.models.co2.P2CO2Hellmann
-
- q - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- Q - Variable in class etomica.potential.P2HePCKLJS
-
- q - Variable in class etomica.potential.P2NitrogenHellmann
-
- q - Variable in class etomica.potential.P3Induction.MyAgent
-
- q - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- q - Variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- q0 - Variable in class etomica.math.Quaternion
-
- q0 - Variable in class org.jmol.util.Quaternion
-
- q1 - Variable in class etomica.math.Quaternion
-
- q1 - Variable in class etomica.potential.P2Electrostatic
-
- q1 - Variable in class etomica.potential.P2ElectrostaticWithHardCore
-
- q1 - Variable in class org.jmol.util.Quaternion
-
- q1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- q1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- q1Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- q2 - Variable in class etomica.math.Quaternion
-
- q2 - Variable in class etomica.potential.P2Electrostatic
-
- q2 - Variable in class etomica.potential.P2ElectrostaticWithHardCore
-
- q2 - Variable in class org.jmol.util.Quaternion
-
- q2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- q2Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- q3 - Variable in class etomica.math.Quaternion
-
- q3 - Variable in class org.jmol.util.Quaternion
-
- q3Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- q4Bond - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- q_err - Variable in class etomica.potential.EwaldSumMolecules
-
- qA - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- qA - Static variable in class etomica.potential.P2NitrogenHellmann
-
- qA - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- qaa - Static variable in class etomica.potential.P2O2Bartolomei
-
- qaaMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- qaaPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- qajmols - Static variable in class etomica.potential.P2O2Bartolomei
-
- qajmolsMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- qajmolsPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- qajp1 - Static variable in class etomica.potential.P2O2Bartolomei
-
- qajp1MRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- qajp1PT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- qajpn - Static variable in class etomica.potential.P2O2Bartolomei
-
- qajpnMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- qajpnPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- qB - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- qB - Static variable in class etomica.potential.P2NitrogenHellmann
-
- qB - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- qbet - Static variable in class etomica.potential.P2O2Bartolomei
-
- qbetMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- qbetPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- qCalc(int, double[]) - Method in class etomica.veos.QSeries
-
Computes Q * N!/V^N based on the volume series for Q given by qCalc.
- qCalc(double, int) - Method in class etomica.veos.Ushcats
-
Computes q, given as Q * N!/V^N, where Q is the configurational integral.
- QFH - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
-
- QFH - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- QFH - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- QFH - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
-
- QH - Static variable in class etomica.models.water.P2WaterSPCE
-
- qH - Static variable in class etomica.models.water.P2WaterTIP4P
-
- Qi - Variable in class etomica.normalmode.IntegratorHarmonic
-
- QO - Static variable in class etomica.models.water.P2WaterSPCE
-
- qp - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- qp - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- qp_q - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- qp_q - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- qq - Variable in class etomica.potential.P2Electrostatic
-
- qq - Variable in class etomica.potential.P2ElectrostaticWithHardCore
-
- Qr - Variable in class etomica.normalmode.IntegratorHarmonic
-
- QSeries - Class in etomica.veos
-
Fluid properties based on direct expansion of the canonical partition function Q in terms
of irreducible cluster integrals beta.
- QSeries(BetaSource) - Constructor for class etomica.veos.QSeries
-
- qSite - Variable in class etomica.potential.P3Induction.MyAgent
-
- qsqv - Variable in class etomica.potential.P2SpheroPolyhedron
-
- qu - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- qu - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- quadId(int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams
-
Returns the quad ID for the given indices (id0, id1, id2, id3) and given
number of molecules (n).
- quadId(int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagramsPT
-
Returns the quad ID for the given indices (id0, id1, id2, id3) and given
number of molecules (n).
- Quadric - Class in org.jmol.util
-
- Quadric(Vector3f[], float[], boolean) - Constructor for class org.jmol.util.Quadric
-
- Quadric(double[]) - Constructor for class org.jmol.util.Quadric
-
- quadStart - Static variable in class etomica.virial.cluster.VirialDiagrams
-
- quadStart - Static variable in class etomica.virial.cluster.VirialDiagramsPT
-
- quality - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Output image quality.
- Quantity - Class in etomica.units.dimensions
-
The dimension for the quantity of discrete things (e.g.
- quantity() - Method in class etomica.units.systems.CGS
-
- quantity() - Method in class etomica.units.systems.LJ
-
- quantity() - Method in class etomica.units.systems.MKS
-
- quantity() - Method in class etomica.units.systems.UnitSystem
-
- quantity() - Method in class etomica.units.systems.UnitSystem.Sim
-
- quat - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion.MoleculeAgent
-
- quaternion - Variable in class etomica.atom.AtomOrientedQuaternion
-
- Quaternion - Class in etomica.math
-
Quaternion object , its properties and associated operations
- Quaternion(double[]) - Constructor for class etomica.math.Quaternion
-
Constructs the Quaternion q = p[0] + p[1]*i + p[2]*j + p[3]*k
- Quaternion(double, Vector) - Constructor for class etomica.math.Quaternion
-
Constructs the Quaternion q = a + b
- Quaternion(Vector, double) - Constructor for class etomica.math.Quaternion
-
Constructs the unit Quaternion q = cos(angle/2) + axis*sin(angle/2)
- Quaternion(double, double, double, double) - Constructor for class etomica.math.Quaternion
-
Constructs the Quaternion q = a + b*i + c*j + d*k
- Quaternion(double, double[]) - Constructor for class etomica.math.Quaternion
-
Constructs the Quaternion q = a + b[0]*i + b[1]*j + b[2]*k
- Quaternion(OrientationFull3D) - Constructor for class etomica.math.Quaternion
-
Constructs the Quaternion q for an input OrientationFull3D with two vectors.
- Quaternion(Vector[]) - Constructor for class etomica.math.Quaternion
-
Constructs the Quaternion q for an input basis vector array.
- Quaternion(Matrix) - Constructor for class etomica.math.Quaternion
-
Constructs the Quaternion q given an input rotation matrix.
- Quaternion - Class in org.jmol.util
-
- Quaternion() - Constructor for class org.jmol.util.Quaternion
-
- quaternionframe - Static variable in class org.jmol.script.Token
-
- quatVelocity - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- quiet - Static variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- quiet - Static variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- quiet - Static variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- quintId(int, int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams
-
Returns the quint ID for the given indices (id0, id1, id2, id3, id4) and given
number of molecules (n).
- quintId(int, int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagramsPT
-
Returns the quint ID for the given indices (id0, id1, id2, id3, id4) and given
number of molecules (n).
- quintStart - Static variable in class etomica.virial.cluster.VirialDiagrams
-
- quintStart - Static variable in class etomica.virial.cluster.VirialDiagramsPT
-
- quit() - Method in interface etomica.graph.engine.ConsoleContainer
-
- quit(Parser.Command) - Method in class etomica.graph.engine.Interpreter
-
- quit() - Method in class etomica.graph.engine.Launcher.ConsoleWindow
-
- quitSearch() - Method in class etomica.dimer.IntegratorDimerMin
-
Called after criteria is met in the rotateDimer method.
R
- r - Variable in class etomica.action.IntegratorDimerApproach
-
- r - Variable in class etomica.association.MCMoveVolumeAssociated
-
- r - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- R - Variable in class etomica.conjugategradient.ConjugateGradients
-
- R - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- R - Variable in class etomica.conjugategradient.SteepestDescent
-
- R - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- r - Variable in class etomica.modules.rheology.ConformationPolymer
-
- r - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- r - Variable in class etomica.modules.sam.P1Sinusoidal
-
- r - Variable in class etomica.virial.simulations.VirialH2OGCPMD.Clusterfoo
-
- r0 - Variable in class etomica.association.MCMoveDimerRotate
-
- r0 - Variable in class etomica.association.MCMoveSmerRotate
-
- r0 - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- r0 - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- r0 - Variable in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- r0 - Variable in class etomica.meam.ParameterSetMEAM
-
- r0 - Variable in class etomica.meam.PotentialCuLREP
-
- r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- r0 - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- R0 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- R0 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- R0 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- R0 - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- r0 - Variable in class etomica.modules.droplet.IntegratorDroplet.MyAgent
-
- r0 - Static variable in class etomica.potential.P2HydrogenHindePatkowski
-
- r0 - Static variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- r0 - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- R0 - Variable in class etomica.potential.P3HydrogenGarberoglioMolecular
-
- r0 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r0 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- r00 - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
-
- r01Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r01Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- r02Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r02Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- R1 - Variable in class etomica.meam.PotentialEAM_LS
-
- R1 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- R1 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- R1 - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- r1 - Variable in class etomica.potential.P3HydrogenATM
-
- r1 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r1 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- r12 - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
-
- r12 - Variable in class etomica.potential.P3QChem.DampingParams
-
- r12Vec - Variable in class etomica.potential.PotentialEmul
-
- r12Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r12Vec - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- R2 - Variable in class etomica.meam.PotentialEAM_LS
-
- r2 - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- r2 - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- r2 - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- r2 - Variable in class etomica.nbr.CriterionSimple
-
- r2 - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- r2 - Variable in class etomica.potential.P3HydrogenATM
-
- r2(Vector1D, Vector1D, Boundary) - Static method in class etomica.space1d.Space1D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2(Vector1D, Vector1D, Boundary, Vector1D) - Static method in class etomica.space1d.Space1D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2(Vector2D, Vector2D, Boundary) - Static method in class etomica.space2d.Space2D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2(Vector2D, Vector2D, Boundary, Vector2D) - Static method in class etomica.space2d.Space2D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2(Vector3D, Vector3D, Boundary) - Static method in class etomica.space3d.Space3D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2(Vector3D, Vector3D, Boundary, Vector3D) - Static method in class etomica.space3d.Space3D
-
Computes the square of the magnitude of the difference of two vectors, subject
to a nearest image transformation.
- r2 - Variable in class etomica.virial.ClusterSumMultibody
-
- r2 - Variable in class etomica.virial.ClusterWheatleyMultibody
-
- r2 - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
-
- r2 - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- r2 - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- r2 - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
-
- r2 - Variable in class etomica.virial.CoordinatePairLeafSet
-
- r2 - Variable in class etomica.virial.CoordinatePairMoleculeSet
-
- r2 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- r2 - Static variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- r2a - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- r2ab - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- r2b - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- r2Core - Variable in class etomica.potential.PotentialEmul
-
- r2Cut - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- r2Cutoff - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- r2Cutoff - Variable in class etomica.potential.P2MoleculeTruncated
-
- r2Cutoff - Variable in class etomica.potential.P2SoftSphericalTruncated
-
- r2Cutoff - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- r2Cutoff - Variable in class etomica.potential.P2SoftTruncated
-
- r2Cuts - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
- r2Cuts - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
- r2d2udr2 - Variable in class etomica.virial.PercusYevick1QC
-
- r2Data - Variable in class etomica.potential.P2QChemInterpolated
-
- r2MaxSafe - Variable in class etomica.nbr.CriterionSimple
-
- r2MaxSafe - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- r2Switch - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- r2Switch - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- R3 - Variable in class etomica.meam.PotentialEAM_LS
-
- r3 - Variable in class etomica.potential.P3HydrogenATM
-
- rAB - Variable in class etomica.potential.EwaldSummation
-
- rac - Variable in class etomica.dimer.P1LepsHarmonic
-
- rAccum - Variable in class etomica.data.meter.MeterMeanSquareDisplacement
-
- radau_f1_tst(Vector[]) - Method in class etomica.potential.P2WaterPotentialsJankowski
-
- Radian - Class in etomica.units
-
Simulation unit for the measure of an angle.
- radiansPerDegree - Static variable in class org.jmol.util.Measure
-
- radiansPerDegree - Static variable in class org.jmol.viewer.JmolConstants
-
- radicalColorMap - Variable in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- radioB - Variable in class etomica.modules.clustergenerator.MyApplet
-
- radioB1 - Variable in class etomica.modules.clustergenerator.MyApplet
-
- radius - Variable in class etomica.math.geometry.Hypersphere
-
- radius - Static variable in class org.jmol.script.Token
-
- random - Variable in class etomica.action.AtomActionRandomizeVelocity
-
- random - Variable in class etomica.association.AtomSourceRandomDimer
-
- random - Variable in class etomica.association.AtomSourceRandomSmer
-
- random - Variable in class etomica.association.ColorSchemeSmer
-
- random - Variable in class etomica.association.ColorSchemeSmerByLength
-
- random - Variable in class etomica.association.MCMoveDimer
-
- random - Variable in class etomica.association.MCMoveDimerRotate
-
- random - Variable in class etomica.association.MCMoveSmer
-
- random - Variable in class etomica.association.MCMoveSmerRotate
-
- random - Variable in class etomica.association.MoleculeSourceRandomDimer
-
- random - Variable in class etomica.atom.AtomSourceRandomLeaf
-
- random - Variable in class etomica.atom.AtomSourceRandomSpecies
-
- random - Variable in class etomica.box.RandomPositionSourceDeformable
-
- random - Variable in class etomica.box.RandomPositionSourceRectangular
-
- random - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- random - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- random - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- random - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- random - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- random - Variable in class etomica.integrator.IntegratorManagerMC
-
- random - Variable in class etomica.integrator.IntegratorMC
-
- random - Variable in class etomica.integrator.IntegratorMD
-
- random - Variable in class etomica.integrator.mcmove.MCMoveAtom
-
- random - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- random - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- random - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- random - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- random - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- random - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- random - Variable in class etomica.models.hexane.MCMoveCBMC
-
- random - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- random - Variable in class etomica.models.hexane.MCMoveReptate
-
- random - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- random - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- random - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- random - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- random - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- random - Variable in class etomica.models.nitrogen.MeterDirectInitPert
-
- random - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- random - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- random - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
-
- random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- random - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
-
- random - Variable in class etomica.modules.adsorption.P1Wall
-
- random - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
-
- random - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeRandom
-
- random - Variable in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
- random - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- random - Variable in class etomica.modules.droplet.ConfigurationDroplet
-
- random - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- random - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- random - Variable in class etomica.modules.rheology.ConformationPolymer
-
- random - Variable in class etomica.molecule.MoleculeSourceRandomMolecule
-
- random - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- random - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- random - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- random - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- random - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
-
- random - Variable in class etomica.normalmode.MCMoveHarmonic
-
- random - Variable in class etomica.normalmode.MCMoveHarmonicStep
-
- random - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- random - Variable in class etomica.normalmode.MCMovePhaseAngle
-
- random - Variable in class etomica.normalmode.MCMoveSingleMode
-
- random - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- random - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- random - Variable in class etomica.normalmode.MCMoveWV
-
- random - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- random - Variable in class etomica.simulation.Simulation
-
- random - Variable in class etomica.spin.MCMoveSpinFlip
-
- random - Variable in class etomica.virial.cluster.ClusterDiagramTree
-
- random - Variable in class etomica.virial.ClusterSumStickyEF
-
- random - Variable in class etomica.virial.ConfigurationClusterAceticAcid
-
- random - Variable in class etomica.virial.ConfigurationClusterMove
-
- random - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- random - Variable in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- random - Variable in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- random - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- random - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- random - Variable in class etomica.virial.MCMoveClusterReptateMulti
-
- random - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- random - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- random - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- random - Variable in class etomica.virial.MCMoveClusterRingScale
-
- random - Variable in class etomica.virial.MeterVirialBDBin
-
- random - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- random - Variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- random - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- random1 - Variable in class etomica.dimer.IntegratorDimerRT
-
- randomAtom0 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- randomAtom1 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- randomDirection(IRandom) - Method in class etomica.space1d.Vector1D
-
- randomizeDiagram() - Method in class etomica.virial.ClusterSumStickyEF
-
set the diagram used for calculating the value to a random one.
- randomizeMomenta() - Method in class etomica.integrator.IntegratorHard
-
Updates collision times appropriately after randomizing momenta
as part of the Andersen thermostat.
- randomizeMomenta() - Method in class etomica.integrator.IntegratorMD
-
Randomizes the velocities of all atoms in the box using values
chosen from a Maxwell-Boltzmann distribution, as in the Andersen
thermostat.
- randomizeMomenta() - Method in class etomica.integrator.IntegratorRigidIterative
-
- randomizeMomenta() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- randomizeMomenta() - Method in class etomica.integrator.IntegratorVerlet
-
Updates MrLast appropriately after randomizing momenta
as part of the Andersen thermostat.
- randomizeMomenta() - Method in class etomica.interfacial.IntegratorFixedWall
-
- randomizeMomenta() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorHard
-
Updates collision time appropriately after randomizing momentum
as part of the Andersen thermostat.
- randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorMD
-
Randomizes the velocities of the given atom using value
chosen from a Maxwell-Boltzmann distribution, as in the Andersen
thermostat.
- randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorRigidIterative
-
- randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- randomizeMomentum(IAtomKinetic) - Method in class etomica.integrator.IntegratorVerlet
-
Updates MrLast appropriately after randomizing momentum
as part of the Andersen thermostat.
- randomizeMomentum(IAtomKinetic) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- randomizePositions() - Method in class etomica.dimer.SimDimerLJadatom
-
- randomizePositions() - Method in class etomica.kmc.IntegratorKMC
-
- randomizePositions() - Method in class etomica.kmc.IntegratorKMCCluster
-
- randomizePositions() - Method in class etomica.kmc.SimKMCLJadatom
-
- randomizePositions() - Method in class etomica.kmc.SimKMCMEAMadatom
-
- randomizer - Variable in class etomica.modules.adsorption.P1Wall
-
- randomizeTotalKE() - Method in class etomica.integrator.IntegratorHard
-
Updates collision times appropriately after randomizing momenta
as part of the Andersen scaling thermostat.
- randomizeTotalKE() - Method in class etomica.integrator.IntegratorMD
-
Scales all velocities so that the total kinetic energy matches a value selected at random for the
previously specified temperature.
- randomLensPoint(Vector, Vector, Vector3D, Vector, double) - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
Sets a given vector to a point chosen uniformly at random in the lens-shaped region
formed by the overlap of two spheres of unit radius located at the given positions r1 and r2.
- randomLensPoint(double, Vector3D) - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
Returns a randomly selected point from within the lens-shaped region of
overlap of two spheres of unit radius separated by a distance d.
- randomLensPointInBox(Vector, Vector, Vector) - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
- RandomMersenneTwister - Class in etomica.util.random
-
Mersenne Twister RNG.
- RandomMersenneTwister(int) - Constructor for class etomica.util.random.RandomMersenneTwister
-
Creates a Mersenne Twister with the given seed.
- RandomMersenneTwister(int[]) - Constructor for class etomica.util.random.RandomMersenneTwister
-
Creates a Mersenne Twister with the given array of seeds.
- randomMol0 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- randomMol1 - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- randomNumber0 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- randomNumber1 - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- RandomNumberGenerator - Class in etomica.util.random
-
Random number generator class.
- RandomNumberGenerator() - Constructor for class etomica.util.random.RandomNumberGenerator
-
- RandomNumberGenerator(long) - Constructor for class etomica.util.random.RandomNumberGenerator
-
- RandomNumberGeneratorUnix - Class in etomica.util.random
-
Random number generator that takes random bits from files.
- RandomNumberGeneratorUnix() - Constructor for class etomica.util.random.RandomNumberGeneratorUnix
-
Create an RNG using /dev/urandom as a source of random bits.
- RandomNumberGeneratorUnix(String) - Constructor for class etomica.util.random.RandomNumberGeneratorUnix
-
Create an RNG using the given file as a source of random bits.
- randomOrientation(Vector) - Method in class etomica.virial.MCMoveClusterPolyhedraChain
-
- randomOrientation(Vector) - Method in class etomica.virial.MCMoveClusterPolyhedraTree
-
- randomPosition() - Method in interface etomica.box.RandomPositionSource
-
Returns a random position with the previously set box's boundary.
- randomPosition() - Method in class etomica.box.RandomPositionSourceDeformable
-
- randomPosition() - Method in class etomica.box.RandomPositionSourceRectangular
-
- randomPosition() - Method in class etomica.space3d.BoundaryTruncatedOctahedron
-
- RandomPositionSource - Interface in etomica.box
-
Interface for an object which returns random positions within a box's
boundary.
- RandomPositionSourceDeformable - Class in etomica.box
-
Implementation of RandomPositionSource that can handle
BoundaryDeformablePeriodic.
- RandomPositionSourceDeformable(Space, IRandom) - Constructor for class etomica.box.RandomPositionSourceDeformable
-
- RandomPositionSourceRectangular - Class in etomica.box
-
- RandomPositionSourceRectangular(Space, IRandom) - Constructor for class etomica.box.RandomPositionSourceRectangular
-
- randomRotation(IRandom, double) - Method in interface etomica.space.IOrientation
-
Perform a rotation by a random amount in the solid angle theta on the
present orientation.
- randomRotation(IRandom, double) - Method in class etomica.space1d.Orientation1D
-
Sets orientation randomly to be +1 or -1.
- randomRotation(IRandom, double) - Method in class etomica.space2d.Orientation2D
-
Applies a random rotation of angle selected uniformly within plus or minus tStep
from the current value.
- randomRotation(IRandom, double) - Method in class etomica.space3d.Orientation3D
-
Applies a random rotation of angle selected uniformly from 0 to tStep.
- randomRotation(IRandom, double) - Method in class etomica.space3d.OrientationFull3D
-
Applies a random rotation of angle selected uniformly from 0 to tStep.
- randomSeeds - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- randomSeeds - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- randomSeeds - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- randomSeeds - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- range - Variable in class etomica.graphics.ColorSchemeTemperature
-
- range - Variable in class etomica.lattice.RectangularLatticeNbrIteratorSquare
-
- range - Variable in class etomica.modules.adsorption.MyMCMove
-
- range - Variable in class etomica.modules.adsorption.P1Wall
-
- range - Variable in class etomica.modules.colloid.P1Wall
-
- range - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- range - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- range - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- range - Variable in class etomica.nbr.cell.NeighborCellManager
-
- range - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- range - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- range - Variable in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- range - Variable in class etomica.nbr.list.PotentialMasterList
-
- range - Static variable in class org.jmol.script.Token
-
- RangeComparator() - Constructor for class etomica.virial.MeterVirialExternalFieldOverlapConfined.RangeComparator
-
- rangedAgentManager - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- rangedAgentManager - Variable in class etomica.nbr.PotentialMasterNbr
-
- rangedAgentManager - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- rangedAgentManager - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- RangePermutator - Class in etomica.graph.iterators
-
This is a facility class that iterates through (maxP1 - minP1 + 1) permutations one at
a time.
- RangePermutator(int, int, int) - Constructor for class etomica.graph.iterators.RangePermutator
-
- rangeselected - Static variable in class org.jmol.script.Token
-
- rasmol - Static variable in class org.jmol.script.Token
-
- RASTERIZER_SECURITY_POLICY - Static variable in class etomica.graph.view.rasterizer.Main
-
URL for Squiggle's security policy file
- RATIO - Static variable in class etomica.data.AccumulatorRatioAverageCovariance
-
- ratio - Variable in class etomica.data.AccumulatorRatioAverageCovariance
-
- RATIO - Static variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- ratio - Variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- ratio - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- RATIO - Static variable in class etomica.overlap.DataOverlap
-
- RATIO_ERROR - Static variable in class etomica.data.AccumulatorRatioAverageCovariance
-
- RATIO_ERROR - Static variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- ratioError - Variable in class etomica.data.AccumulatorRatioAverageCovariance
-
- ratioError - Variable in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- ratioErrorStat - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- ratioMaxN - Variable in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- Rational - Class in etomica.math
-
Class handling rational numbers (numerator / denominator), including
addition, multiplication and reducing (15/6 => 5/2).
- Rational() - Constructor for class etomica.math.Rational
-
- Rational(int, int) - Constructor for class etomica.math.Rational
-
Creates Rational instance with the given numerator and denominator.
- Rational - Class in etomica.veos.bigdecimal
-
Fractions (rational numbers).
- Rational() - Constructor for class etomica.veos.bigdecimal.Rational
-
Default ctor, which represents the zero.
- Rational(BigInteger, BigInteger) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from a numerator and denominator.
- Rational(BigInteger) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from a numerator.
- Rational(int, int) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from a numerator and denominator.
- Rational(int) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from an integer.
- Rational(String) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from a string representation.
- Rational(String, int) - Constructor for class etomica.veos.bigdecimal.Rational
-
ctor from a string representation in a specified base.
- ratios - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- ratioStat - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- RAW_RGB - Static variable in class org.jmol.util.Colix
-
- rawData - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- rawData - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- rawData2 - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- rawData2 - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- rawData3 - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- rawData3 - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- rawDataBlockSize - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- rawDataBlockSize - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- RawDataWindowOpener(int, DisplayPlot) - Constructor for class etomica.graphics.DisplayPlot.RawDataWindowOpener
-
- rBond - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- rBound(double, int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
helper method that returns the position r if there are no bounds or
if r is inside the bounds or (if r is outside the bounds) returns the
position in the bounds nearest r.
- rc - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
-
- rc - Variable in class etomica.mappedRdf.MappedRdf.LJMDParams
-
- rc - Variable in class etomica.mappedvirial.MappedU.LJMDParams
-
- rc - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
-
- rc - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
-
- rc - Variable in class etomica.metastable.LJmuVT.LJMCParams
-
- rc - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- rc - Variable in class etomica.metastable.LJNVT.LJMCParams
-
- rC - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- rC - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- rC - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- rC - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- rC - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- rC - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- rC - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- rC - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- rC - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- rc - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
-
- rc - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.MinimizeHCP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- rc - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- rc - Variable in class etomica.parser.ParserLAMMPS.Options
-
- rc0 - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- rc0 - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- rC1 - Variable in class etomica.meam.PotentialCuLREP
-
- rC1 - Variable in class etomica.meam.PotentialEAM
-
- rC1 - Variable in class etomica.meam.PotentialEAM_LS
-
- rc12 - Variable in class etomica.meam.P2EAM
-
- rC2 - Variable in class etomica.meam.PotentialCuLREP
-
- rC2 - Variable in class etomica.meam.PotentialEAM
-
- rC2 - Variable in class etomica.meam.PotentialEAM_LS
-
- rc22 - Variable in class etomica.meam.P2EAM
-
- rCc - Variable in class etomica.meam.PotentialEFS
-
- rCd - Variable in class etomica.meam.PotentialEFS
-
- RcData - Variable in class etomica.potential.P2QChemInterpolated
-
- rcLong - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- rcMax0 - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- rcMax0 - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- rcMax1 - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- rcMax1 - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- rcond - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- rcScale - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- rcScale - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- rcScale - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- rcShort - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
-
- rcShort - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- rcShort - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- rCut - Variable in class etomica.models.water.P2Water4P
-
- rCut - Variable in class etomica.potential.EwaldSumMolecules
-
- rCut2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- rCut2 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- rCut2 - Variable in class etomica.potential.Potential2SoftSphericalLS
-
- rCut2 - Variable in class etomica.virial.ClusterWheatleyMultibody
-
- rCut2 - Variable in class etomica.virial.ClusterWheatleyMultibodyBD
-
- rCut2 - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- rCut2 - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- rCut2 - Variable in class etomica.virial.ClusterWheatleyMultibodyMix
-
- rCutLJ - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- rCutLJ - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- rCutMax - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- rCutMax - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- rCutoff - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- rCutoff - Variable in class etomica.potential.P2MoleculeTruncated
-
- rCutoff - Variable in class etomica.potential.P2SoftSphericalTruncated
-
- rCutoff - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- rCutoff - Variable in class etomica.potential.P2SoftTruncated
-
- rCutRealES - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- rCutRealES - Variable in class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- rCutRealES - Variable in class etomica.potential.EwaldSummation
-
- rCutSquared - Variable in class etomica.potential.EwaldSummation
-
- rD - Variable in class etomica.data.meter.MeterPressureTensor
-
- rData - Variable in class etomica.data.meter.MeterRDF
-
- rData - Variable in class etomica.data.meter.MeterRDFPC
-
- rData - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- rData - Variable in class etomica.potential.P2QChemInterpolated
-
- rdfdr - Variable in class etomica.virial.HypernettedChain
-
- rdfdr - Variable in class etomica.virial.PercusYevick
-
- rdfListener - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- rdfPump - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- rDistributionErrorHash - Variable in class etomica.virial.CalcFFT
-
- rDistributionHash - Variable in class etomica.virial.CalcFFT
-
- rdudr - Variable in class etomica.virial.PercusYevick1QC
-
- re - Static variable in class etomica.potential.P1HydrogenMielke
-
- ReactionEquilibrium - Class in etomica.modules.reactionequilibrium
-
- ReactionEquilibrium() - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- ReactionEquilibriumGraphic - Class in etomica.modules.reactionequilibrium
-
- ReactionEquilibriumGraphic(ReactionEquilibrium, Space) - Constructor for class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
-
- ReactionEquilibriumGraphic.Applet - Class in etomica.modules.reactionequilibrium
-
- ReactionEquilibriumGraphic.MassEditor - Class in etomica.modules.reactionequilibrium
-
- ReactionEquilibriumGraphic.MySpeciesEditor - Class in etomica.modules.reactionequilibrium
-
- reactionField - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- reactionManagerCO - Variable in class etomica.modules.catalysis.Catalysis
-
- ReactionManagerCO - Class in etomica.modules.catalysis
-
- ReactionManagerCO(Catalysis) - Constructor for class etomica.modules.catalysis.ReactionManagerCO
-
- read(String) - Method in interface etomica.graph.engine.ConsoleReader
-
- read(String) - Method in class etomica.graph.engine.Interpreter
-
- read(Parser.CommandVariableValue) - Method in class etomica.graph.engine.Interpreter
-
- readData(String[]) - Method in class etomica.virial.MeterVirialBDBin
-
- readData(String[]) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- readData(String[]) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- readData(String[], int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- readData(String[], int, boolean) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- readDataReBin(String[], int, int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- readdb(Parser.CommandValue) - Method in class etomica.graph.engine.Interpreter
-
- readDistribution(int, boolean) - Method in class etomica.virial.CalcFFT
-
- ReaderIn - Class in etomica.eigenstuff
-
Reads in a file.
- ReaderIn() - Constructor for class etomica.eigenstuff.ReaderIn
-
- readFile(String, double[][]) - Static method in class etomica.math.numerical.AkimaSplineSmootherApp
-
- readFile(String, double[][]) - Static method in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- readFile(String, double[][]) - Static method in class etomica.math.numerical.AkimaSplineSmootherMain
-
- readLine(PipedInputStream) - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
-
- readMethod - Variable in class etomica.modifier.ModifierGeneral
-
- readOutputFile() - Method in class etomica.potential.PotentialEmul
-
- ReadParameters - Class in etomica.util
-
This class reads input parameters from a file and assigns the values to the
fields of an object.
- ReadParameters() - Constructor for class etomica.util.ReadParameters
-
- ReadParameters(String) - Constructor for class etomica.util.ReadParameters
-
- ReadParameters(String, ParameterBase) - Constructor for class etomica.util.ReadParameters
-
- readParameters() - Method in class etomica.util.ReadParameters
-
Reads each line from inputFileName and attempts to match it with a field
from parameterWrapper and sets the field to the value from the file.
- readProcessData(String, int) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- readResolve() - Method in class etomica.graph.view.rasterizer.DestinationType
-
- readWeights(String) - Method in class etomica.virial.MeterVirialBDBin
-
- readWeights(String) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- readWeights(String) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- readWeights(String, int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- readWriteData(String[], String, int) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
This method reads all input files in parallel and writes lines out to
the new file as the bin data is known to be complete.
- ready - Variable in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
-
- real() - Method in class etomica.math.Complex
-
Real part of this Complex number, the x-coordinate in rectangular coordinates.
- realT - Variable in class etomica.normalmode.MeterHarmonicCoordinate
-
- realT - Variable in class etomica.normalmode.MeterHarmonicEnergy
-
- realT - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- realT - Variable in class etomica.normalmode.MeterNormalMode
-
- reblockData() - Method in class etomica.data.AccumulatorAverageBootstrap
-
Reblock data from rawData2 into rawData3, then copy it back to rawData2
- reblockData(int) - Method in class etomica.data.AccumulatorAverageBootstrap
-
Brute-force reblock data from rawData into rawData2,
taking blocks of size n
- reblockData() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Reblock data from rawData2 into rawData3, then copy it back to rawData2
- reblockData(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Reblock data from rawData into rawData2, taking blocks of size n
- Reciprocal() - Constructor for class etomica.math.function.Function.Reciprocal
-
- reclaim(IAtom) - Method in class etomica.association.ColorSchemeSmer
-
- recomputeColumnHeaders() - Method in class etomica.graphics.DisplayTable
-
Reconstruct the column headers array.
- recomputeCriteriaRanges() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Recomputes the range for all criterion based on our own range.
- recomputeCriteriaRanges() - Method in class etomica.nbr.list.PotentialMasterList
-
Recomputes the range for all criterion based on our own range.
- recomputeMoveFrequencies() - Method in class etomica.integrator.mcmove.MCMoveManager
-
Recomputes all the move frequencies.
- recomputeUnits() - Method in class etomica.graphics.DisplayTable
-
Reconstruct the units array.
- recomputeWeights() - Method in class etomica.virial.MeterVirialBDBin
-
- recomputeWeights() - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, long) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, long, boolean) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
This method will read MyData.unscreenedCount and MyData.accumulator
and write to MyData.weight.
- recomputeWeights() - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialBinMultiThreaded.MyData>, long) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialBinMultiThreaded.MyData>, long, boolean) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
-
This method will read MyData.unscreenedCount and MyData.accumulator
and write to MyData.weight.
- recomputeWeights() - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, long, int) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- recomputeWeights(Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, long, boolean, int) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
This method will read MyData.unscreenedCount and MyData.accumulator
and write to MyData.weight.
- reconfig - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- reconfig - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- Rectangle - Class in etomica.math.geometry
-
A 2-dimensional geometric rectangle.
- Rectangle(Space) - Constructor for class etomica.math.geometry.Rectangle
-
Constructs a square rectangle of unit size.
- Rectangle(Space, double, double) - Constructor for class etomica.math.geometry.Rectangle
-
Constructs a rectangle with edge lengths having the given values.
- RECTANGLE - Static variable in class g3dsys.control.G3DSys
-
- RectangleOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.RectangleOptionHandler
-
- Rectangular - Interface in etomica.math.geometry
-
Interface for a polytope with shape that can be specified by the length
of D sides.
- RectangularLattice - Class in etomica.lattice
-
Basic implementation of the AbstractLattice interface, providing construction
and access of sites for a lattice of arbitrary dimension.
- RectangularLattice(int, SiteFactory) - Constructor for class etomica.lattice.RectangularLattice
-
Constructs a lattice of the given dimension (D) with sites
made from the given factory.
- RectangularLattice.Iterator - Class in etomica.lattice
-
Iterates over all sites of the lattice.
- RectangularLatticeNbrIterator - Class in etomica.lattice
-
An abstract iterator that generates the neighboring sites of a given site.
- RectangularLatticeNbrIterator(int) - Constructor for class etomica.lattice.RectangularLatticeNbrIterator
-
Constructs iterator that needs to be configured before use.
- RectangularLatticeNbrIteratorAdjacent - Class in etomica.lattice
-
Iterates over the neighbors of a site, where neighbors are those
sites immediately adjacent to it in each direction; this does not
include sites diagonal to the site.
- RectangularLatticeNbrIteratorAdjacent(int) - Constructor for class etomica.lattice.RectangularLatticeNbrIteratorAdjacent
-
- RectangularLatticeNbrIteratorSquare - Class in etomica.lattice
-
Iterates over neighbors of a site, where neighbors are defined as
those sites lying in a rectangular region centered on the site.
- RectangularLatticeNbrIteratorSquare(int) - Constructor for class etomica.lattice.RectangularLatticeNbrIteratorSquare
-
- recursiveTag(IAtom, int) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- recursiveTag(IAtom, int) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- recursiveTag(IAtom) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- RED - Static variable in class org.jmol.util.Colix
-
- redColorScheme - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- redistributeForces(IMolecule, AtomLeafAgentManager<IntegratorVelocityVerlet.MyAgent>) - Method in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
-
- redomove - Static variable in class org.jmol.script.Token
-
- reduce(long, long) - Method in class etomica.graph.model.impl.CoefficientImpl
-
- reduce(ArrayList<ClusterDiagram>) - Static method in class etomica.virial.cluster.ClusterOperations
-
Sorts cluster diagrams (but # of connections) and combines any diagrams
that are identical, resulting in a diagram with a weight equal to the
sum of the original weights.
- reducedTemp - Variable in class etomica.virial.CalcFFT
-
- ReeHoover - Class in etomica.graph.operations
-
This operation performs conversion from a set of biconnected graphs with f
edges to a set of diagrams of fully connected diagrams with e and f edges.
- ReeHoover() - Constructor for class etomica.graph.operations.ReeHoover
-
- ReeHoover.ReeHooverParameters - Class in etomica.graph.operations
-
- reeHooverCB - Variable in class etomica.modules.clustergenerator.MyApplet
-
- ReeHooverMC - Class in etomica.virial.simulations
-
An implementation of MSMC with direct sampling for computation of
virial coefficients of hard spheres, in the spirit of Ree-Hoover Monte Carlo
(Ree & Hoover, 1964, Fifth and Sixth Virial Coefficients for Hard Spheres and
Hard Disks).
- ReeHooverMC() - Constructor for class etomica.virial.simulations.ReeHooverMC
-
- ReeHooverMC.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- ReeHooverParameters(char) - Constructor for class etomica.graph.operations.ReeHoover.ReeHooverParameters
-
- ReeHooverToggler() - Constructor for class etomica.modules.clustergenerator.MyApplet.ReeHooverToggler
-
- ref - Variable in class etomica.liquidLJ.DataProcessorReweightRatio
-
- REF - Static variable in class etomica.overlap.DataOverlap
-
- ref - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- ref - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- ref - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- ref - Variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- ref - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- ref - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- ref - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- refAccumulator - Variable in class etomica.virial.overlap.DataSourceVirialOverlap
-
- refAccumulator - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- refAvg - Variable in class etomica.overlap.DataOverlap
-
- refAvg - Variable in class etomica.virial.overlap.DataVirialOverlap.FullResult
-
- reference - Variable in class etomica.compatibility.FeatureRequirement
-
- referenceDataInterval - Variable in class etomica.normalmode.SimOverlapModule
-
- refErr - Variable in class etomica.virial.overlap.DataVirialOverlap.FullResult
-
- refFrac - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialB3C1TIP4Pwater.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialB3C2TIP4Pwater.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialH2OGCPMD.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialLJD.VirialLJParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
-
- refFrac - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
-
- refFrac - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- refFreq - Variable in class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
-
- refFreq - Variable in class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
-
- refFreq - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
-
- refFreq - Variable in class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
-
- refFreq - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
-
- reflect() - Method in class etomica.normalmode.MeterSolidMirror
-
- refPref - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- refPref - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- refPref - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- refPref - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- refPref - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- refPref - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- refPref - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- refPref - Variable in class etomica.normalmode.MeterSamplingHarmonic
-
- refPref - Variable in class etomica.normalmode.MeterSamplingTarget
-
- refPref - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
-
- refPref - Variable in class etomica.normalmode.MeterWorkBennetTarget
-
- refPref - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
-
- refPref - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- refPref - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- refPref - Variable in class etomica.normalmode.MeterWorkTargetBennet
-
- refPref - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- refPref - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
-
- refPref - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- refPref - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- refPref - Variable in class etomica.normalmode.SimBennet
-
- refPref - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- refPref - Variable in class etomica.normalmode.SimOverlap
-
- refPref - Variable in class etomica.normalmode.SimOverlapLJ
-
- refPref - Variable in class etomica.normalmode.SimOverlapLJModule
-
- refPref - Variable in class etomica.normalmode.SimOverlapSoftSphere
-
- refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- refPref - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- refPref - Variable in class etomica.normalmode.SimOverlapSSnxy
-
- refPref - Variable in class etomica.normalmode.SimTargetUmbrella
-
- refPref - Variable in class etomica.normalmode.SimUmbrella
-
- refPref - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- refPref - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- refPref - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- refPref - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- refPrefFileName - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- refPrefFileName - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- refPrefFileName - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- refresh() - Method in class etomica.graphics.DevicePlotPoints
-
Instructs the plot to redisplay any plotted functions with the most
recent data.
- refresh() - Method in class g3dsys.control.G3DSys
-
For a thorough redraw of the display
- refreshAtomAgentMgr() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
refreshAtomAgentMgr() - sets the new atom manager based upon the box.
- refreshing - Static variable in class org.jmol.script.Token
-
- refreshSize() - Method in class etomica.graphics.DisplayBoxCanvas1D
-
- refreshSize() - Method in class etomica.graphics.DisplayBoxCanvas2D
-
- refreshSize() - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
- refShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- refShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- refShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- refSum - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- rejectNotify() - Method in class etomica.association.MCMoveBiasUB
-
- rejectNotify() - Method in class etomica.association.MCMoveBiasUBMolecule
-
- rejectNotify() - Method in class etomica.association.MCMoveDimer
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.association.MCMoveDimerRotate
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.association.MCMoveRotateAssociated
-
- rejectNotify() - Method in class etomica.association.MCMoveSmer
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.association.MCMoveSmerRotate
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.association.MCMoveVolumeAssociated
-
- rejectNotify() - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- rejectNotify() - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMove
-
Method called by IntegratorMC in the event that the most recent trial
move is rejected.
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveAtom
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveBoxSize
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveDimer
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveRotate
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
-
Performs no action; nothing required when move rejected.
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveVolumeExchange
-
- rejectNotify() - Method in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- rejectNotify() - Method in class etomica.interfacial.MCMoveAtomNbr
-
- rejectNotify() - Method in class etomica.models.hexane.MCMoveCBMC
-
- rejectNotify() - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- rejectNotify() - Method in class etomica.models.hexane.MCMoveReptate
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- rejectNotify() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- rejectNotify() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- rejectNotify() - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- rejectNotify() - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- rejectNotify() - Method in class etomica.modules.adsorption.MyMCMove
-
- rejectNotify() - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveAtomCoupled
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.normalmode.MCMoveAtomSuperBox
-
Method called by IntegratorMC in the event that the most recent trial move is
rejected.
- rejectNotify() - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveHarmonic
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveHarmonicStep
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
- rejectNotify() - Method in class etomica.normalmode.MCMovePhaseAngle
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveSingleMode
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- rejectNotify() - Method in class etomica.normalmode.MCMoveWV
-
- rejectNotify() - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- rejectNotify() - Method in class etomica.spin.MCMoveSpinFlip
-
- rejectNotify() - Method in class etomica.virial.BoxCluster
-
Informs the box that the trial was rejected so it will go back to
the old coordinate pairs.
- rejectNotify() - Method in class etomica.virial.MCMoveChangeBondLength
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAngleBend
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtom
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomChainHSTail
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomDiscrete
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomHSChain
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomHSTree
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomQ
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterDiagram
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterMolecule
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterMoleculeMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraChain
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterPolyhedraTree
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRingRegrow
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRingScale
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRotateCH3
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- rejectNotify() - Method in class etomica.virial.MCMoveClusterWiggleMulti
-
- rejectNotify() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
-
- Relabel - Class in etomica.graph.operations
-
- Relabel() - Constructor for class etomica.graph.operations.Relabel
-
- relabel - Variable in class etomica.graph.property.FFTDecomposition
-
- relabel - Variable in class etomica.graph.property.IsFFT
-
- relabel(Graph) - Static method in class etomica.virial.IEGenerator
-
- RelabelParameters - Class in etomica.graph.operations
-
- RelabelParameters(byte[]) - Constructor for class etomica.graph.operations.RelabelParameters
-
- RelabelWertheim - Class in etomica.graph.operations
-
- RelabelWertheim() - Constructor for class etomica.graph.operations.RelabelWertheim
-
- relax() - Method in class etomica.space3d.OrientationFull3D
-
Normalizes both direction and secondaryDirection
- relaxAction - Variable in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- relaxInterval - Variable in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- relaxMolecule(IMolecule) - Method in class etomica.integrator.IntegratorVelocityVerletShake.BondConstraints
-
- releaseAgent(ActionMinimizeEnergy.MyForceTorque, IAtom, Box) - Method in class etomica.action.ActionMinimizeEnergy
-
- releaseAgent(AtomArrayList, IAtom, Box) - Method in class etomica.association.AssociationManager
-
- releaseAgent(Object, IMolecule) - Method in class etomica.association.AssociationManagerMolecule
-
- releaseAgent(ColorSchemeSmer.ColorAgent, IAtom, Box) - Method in class etomica.association.ColorSchemeSmer
-
- releaseAgent(MCMoveVolumeAssociated.Agent, IAtom, Box) - Method in class etomica.association.MCMoveVolumeAssociated
-
- releaseAgent(Object, IMolecule) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- releaseAgent(E, IAtom, Box) - Method in interface etomica.atom.AtomLeafAgentManager.AgentSource
-
This informs the agent source that the agent is going away and that
the agent source should disconnect the agent from other elements.
- releaseAgent(E, AtomType) - Method in interface etomica.atom.AtomTypeAgentManager.AgentSource
-
This informs the agent source that the agent is going away and that the agent source should disconnect the
agent from other elements.
- releaseAgent(E) - Method in interface etomica.box.BoxAgentManager.BoxAgentSource
-
Disconnects the given agent from its box and performs any actions needed to clean up
- releaseAgent(AtomLeafAgentManager<E>) - Method in class etomica.box.BoxAgentSourceAtomManager
-
- releaseAgent(MoleculeAgentManager<E>) - Method in class etomica.box.BoxAgentSourceMoleculeManager
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.conjugategradient.DerivativeEnergyFunction.MyAgentSource
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG.MyAgentSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.dimer.IntegratorDimerMin
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.dimer.IntegratorDimerRT
-
- releaseAgent(Object, IAtom, Box) - Method in class etomica.dimer.IntegratorEnergyMap
-
- releaseAgent(ArrayList, IAtom, Box) - Method in class etomica.graphics.BondListener
-
- releaseAgent(Color, IAtom, Box) - Method in class etomica.graphics.ColorSchemeCollectiveAgent
-
- releaseAgent(Color, IAtom, Box) - Method in class etomica.graphics.ColorSchemeRandom
-
- releaseAgent(Object, IMolecule) - Method in class etomica.graphics.ColorSchemeRandomByMolecule
-
- releaseAgent(Ball[], IAtom, Box) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys.OrientedAgentSource
-
- releaseAgent(Figure, IAtom, Box) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- releaseAgent(IntegratorConNVT.Agent, IAtom, Box) - Method in class etomica.integrator.IntegratorConNVT
-
- releaseAgent(IntegratorGear4.Agent, IAtom, Box) - Method in class etomica.integrator.IntegratorGear4
-
- releaseAgent(IntegratorHard.Agent, IAtom, Box) - Method in class etomica.integrator.IntegratorHard
-
- releaseAgent(Vector, IAtom, Box) - Method in class etomica.integrator.IntegratorMD.VectorSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.integrator.IntegratorRigidIterative
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.integrator.IntegratorRigidIterative
-
- releaseAgent(Object, ISpecies) - Method in class etomica.integrator.IntegratorRigidIterative
-
- releaseAgent(IntegratorRigidMatrixIterative.AtomAgent, IAtom, Box) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- releaseAgent(Object, IMolecule) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- releaseAgent(Object, ISpecies) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- releaseAgent(Object, ISpecies) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- releaseAgent(IntegratorVerlet.Agent, IAtom, Box) - Method in class etomica.integrator.IntegratorVerlet
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.mappedvirial.MeterMappedU
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.mappedvirial.MeterMappedVirial
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.mappedvirial.MeterMappedVirialV
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.mappedvirial.MeterMeanForce
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.math.numerical.CalcGradientDifferentiable
-
- releaseAgent(EwaldSummation.MyCharge, IAtom, Box) - Method in class etomica.models.clathrates.MinimizationTIP4P.ChargeAgentSourceRPM
-
- releaseAgent(Object, IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen.OrientationAgentSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox.OrientationAgentSource
-
- releaseAgent(EwaldSummation.MyCharge, IAtom, Box) - Method in class etomica.models.water.ChargeAgentSourceTIP4PWater
-
- releaseAgent(InteractionTracker.CatalysisAgent, IAtom, Box) - Method in class etomica.modules.catalysis.InteractionTracker
-
- releaseAgent(AtomFilterChainLength.LengthAgent, IAtom, Box) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- releaseAgent(IAtom[], IAtom, Box) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- releaseAgent(ColorSchemeRadical.LengthAgent, IAtom, Box) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- releaseAgent(Object, AtomType) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
-
- releaseAgent(IAtom[], IAtom, Box) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- releaseAgent(MeterChainLength.AtomTag, IAtom, Box) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- releaseAgent(Boolean, IAtom, Box) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- releaseAgent(IntegratorDroplet.MyAgent, IAtom, Box) - Method in class etomica.modules.droplet.IntegratorDroplet
-
- releaseAgent(IAtom, IAtom, Box) - Method in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- releaseAgent(Object, IMolecule) - Method in class etomica.modules.rosmosis.MeterFlux
-
- releaseAgent(Vector, IAtom, Box) - Method in class etomica.modules.rosmosis.P1Tether
-
- releaseAgent(Object, IMolecule) - Method in class etomica.modules.sam.CriterionTether3
-
- releaseAgent(E, IMolecule) - Method in interface etomica.molecule.MoleculeAgentManager.MoleculeAgentSource
-
This informs the agent source that the agent is going away and that
the agent source should disconnect the agent from other elements
- releaseAgent(NeighborCellManager) - Method in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- releaseAgent(NeighborCellManagerMolecular) - Method in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- releaseAgent(Object, IMolecule) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Removes the given atom from the cell.
- releaseAgent(Cell, IAtom, Box) - Method in class etomica.nbr.cell.NeighborCellManager
-
Removes the given atom from the cell.
- releaseAgent(CriterionPositionWall.DoubleWrapper, IAtom, Box) - Method in class etomica.nbr.CriterionPositionWall
-
- releaseAgent(Vector, IAtom, Box) - Method in class etomica.nbr.CriterionSimple
-
- releaseAgent(Object, IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular.MoleculePotential1ListSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- releaseAgent(NeighborListManagerMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- releaseAgent(AtomPotentialList, IAtom, Box) - Method in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
-
- releaseAgent(AtomNeighborLists, IAtom, Box) - Method in class etomica.nbr.list.NeighborListManager
-
- releaseAgent(NeighborListManager) - Method in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- releaseAgent(AtomSite, IAtom, Box) - Method in class etomica.nbr.site.NeighborSiteManager
-
- releaseAgent(Vector, IAtom, Box) - Method in class etomica.normalmode.CoordinateDefinition.SiteSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMolecule.MoleculeSiteSource
-
- releaseAgent(Object, IMolecule) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation.MoleculeSiteSource
-
- releaseAgent(HSNPT.MyAgent, IAtom, Box) - Method in class etomica.normalmode.HSNPT.ActionSummer
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.normalmode.MeterDADB
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.normalmode.MeterSolidProps
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.normalmode.MeterSolidPropsLJ
-
- releaseAgent(Object, IAtom, Box) - Method in class etomica.paracetamol.ChargeAgentSourceParacetamol
-
- releaseAgent(Object, IMolecule) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol.OrientationAgentSource
-
- releaseAgent(P2HardBondedList.BondArrayList, IAtom, Box) - Method in class etomica.potential.P2HardBondedList
-
- releaseAgent(AtomArrayList, IAtom, Box) - Method in class etomica.potential.P2SquareWellRobust
-
- releaseAgent(PotentialArrayByType, AtomType) - Method in class etomica.potential.PotentialMasterMonatomic
-
- releaseAgent(IntegratorVelocityVerletQuaternion.AtomAgent, IAtom, Box) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- releaseAgent(Object, IMolecule) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- releaseAgent(Object, ISpecies) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- releaseAgent(E, ISpecies) - Method in interface etomica.species.SpeciesAgentManager.AgentSource
-
This informs the agent source that the agent is going away and that
the agent source should disconnect the agent from other elements.
- releaseAgent(Integrator.Forcible, IAtom, Box) - Method in class etomica.surfacetension.SurfaceTensionMapped
-
- releaseAgent(NeighborCellManagerThreaded) - Method in class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
-
- releaseAgent(IntegratorVelocityVerlet.MyAgent, IAtom, Box) - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- releaseBond(Object) - Method in interface etomica.graphics.BondManager
-
Notifies the BondManager that the given bond no longer exists in the
system.
- releaseBond(Object) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Removes the given bond from the graphical display.
- releaseScreenImage() - Method in class org.jmol.g3d.Graphics3D
-
- releaseScreenImage() - Method in class org.jmol.util.GData
-
- remove(int) - Method in class etomica.atom.AtomArrayList
-
This removes the atom at the given index and shifts the remaining atoms
back (maintaining the order).
- remove() - Method in class etomica.graph.iterators.CartesianIterator
-
- remove() - Method in class etomica.graph.iterators.CartesianPermutator
-
- remove() - Method in class etomica.graph.iterators.ChainedIterator
-
- remove() - Method in class etomica.graph.iterators.DefaultIterator
-
- remove() - Method in class etomica.graph.iterators.DefaultPermutator
-
- remove() - Method in class etomica.graph.iterators.EdgelessIterator
-
- remove() - Method in class etomica.graph.iterators.filters.GlobalFilter
-
- remove() - Method in class etomica.graph.iterators.filters.LocalFilter
-
- remove() - Method in class etomica.graph.iterators.FixedEdgeCountIterator
-
- remove() - Method in class etomica.graph.iterators.IteratorWrapper
-
- remove() - Method in class etomica.graph.iterators.RangePermutator
-
- remove() - Method in class etomica.graph.iterators.StoredIterator
-
- remove(Object) - Method in class etomica.graph.model.GraphList
-
- remove(Display) - Method in class etomica.graphics.SimulationGraphic
-
- remove(Device) - Method in class etomica.graphics.SimulationGraphic
-
- remove(IFunction) - Method in class etomica.math.function.FunctionChain
-
Removes the given function from the chain.
- remove(int) - Method in class etomica.molecule.MoleculeArrayList
-
- remove(int) - Method in class etomica.potential.P2HardBondedList.BondArrayList
-
- remove(Object) - Method in class etomica.util.collections.IndexMap
-
- remove(int) - Method in class etomica.util.collections.IndexMap
-
- remove() - Method in class etomica.util.TreeLinker
-
Disconnects this linker from the linkers above and below it, and
puts them in sequence, repairing the hole.
- remove(TreeLinker) - Static method in class etomica.util.TreeList
-
- remove() - Method in class etomica.virial.PYGenerator.IteratorEF
-
- removeAction(IAction) - Method in interface etomica.action.ActionGroup
-
Removes a specified action from the group.
- removeAction(IAction) - Method in class etomica.action.ActionGroupSeries
-
- removeAction(IAction) - Method in class etomica.action.activity.ActivityGroupParallel
-
- removeAction(IAction) - Method in class etomica.action.activity.ActivityGroupSeries
-
Removes the given action from the list of actions performed by this controller.
- removeAction(IAction) - Method in class etomica.action.activity.Controller
-
- removeAll(Collection<?>) - Method in class etomica.graph.model.GraphList
-
- removeAllValueChangedListeners() - Method in class etomica.graphics.DeviceBox
-
Removes all objects that are listening for a value changed event.
- removeAndReplace(int) - Method in class etomica.atom.AtomArrayList
-
This removes the atom at the given index and replaces the hole with the
last atom.
- removeAndReplace(int) - Method in class etomica.molecule.MoleculeArrayList
-
- removeAtom(IAtom) - Method in class etomica.nbr.cell.Cell
-
- removeAtoms(double, Vector) - Method in class etomica.dimer.SimDimerLJadatom
-
- removeAtoms(double, Vector) - Method in class etomica.dimer.SimDimerMEAMadatom
-
- removeAtoms(double, Vector) - Method in class etomica.dimer.SimDimerMEAMGB
-
- removeAtoms(double, Vector) - Method in class etomica.kmc.SimKMCLJadatom
-
- removeAtoms(double, Vector) - Method in class etomica.kmc.SimKMCMEAMadatom
-
- removeBox(Box) - Method in class etomica.simulation.Simulation
-
Removes a Box to the simulation.
- removeChildAtom(IAtom) - Method in class etomica.molecule.Molecule
-
Removes the given child Atom from this AtomGroup.
- removeChildType(AtomType) - Method in class etomica.species.Species
-
- removeChildType(AtomType) - Method in class etomica.species.SpeciesSpheresHetero
-
Removes the given factory as a child of this factory.
- removeCollisionListener(IntegratorHard.CollisionListener) - Method in class etomica.integrator.IntegratorHard
-
De-registers an object from the list of collision listeners.
- removeCountOfSpeciesSLMListener(int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removeData() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- removeData() - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- removeData() - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- removeDataListener(DataSetListener) - Method in class etomica.data.DataSet
-
- removeDataSink(IDataSink) - Method in class etomica.data.DataFork
-
- removeDataSink(IDataSink) - Method in interface etomica.data.DataPipeForked
-
Removes the specified data sink.
- removeDataSink(IDataSink) - Method in class etomica.data.DataProcessorForked
-
Removes the specified data sink.
- removeDrawable(Drawable) - Method in class etomica.graphics.DisplayBox
-
- removeDrawable(Object) - Method in class etomica.graphics.DisplayBox
-
- removeFig(Figure) - Method in class g3dsys.control.G3DSys
-
Removes the Figure to from associated FigureManager
- removeIntegrator(Integrator) - Method in class etomica.integrator.IntegratorManagerMC
-
Removes the given integrator from the list of integrators.
- removeLine(LineSegment) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- removeListener(BoxEventListener) - Method in class etomica.box.BoxEventManager
-
- removeListener(IntegratorListener) - Method in class etomica.integrator.IntegratorEventManager
-
Removes the given listener from this event manager.
- removeListener(IntegratorListener) - Method in class etomica.integrator.IntegratorListenerGroupSeries
-
Removes the given listener from the group.
- removeListener(INeighborListListenerMolecular) - Method in class etomica.nbr.list.molecule.NeighborListEventManagerMolecular
-
- removeListener(INeighborListListener) - Method in class etomica.nbr.list.NeighborListEventManager
-
- removeListener(SimulationListener) - Method in class etomica.simulation.SimulationEventManager
-
- removeListener(BoundaryEventListener) - Method in class etomica.space.BoundaryEventManager
-
Removes the given listener from this event manager.
- removeListener(IListener<E>) - Method in class etomica.util.EventManager
-
Removes the given listener from this event manager.
- removeMCMove(MCMove) - Method in class etomica.integrator.mcmove.MCMoveManager
-
Removes the given MCMove from the set of moves performed by the integrator and
recalculates move frequencies.
- removeModel(Model) - Method in class etomica.graphics.BondListener
-
Informs the BondListener that bonds in molecules of the given model
should no longer be tracked.
- removeMolecule(IMolecule) - Method in class etomica.box.Box
-
Removes the given molecule from this Box.
- removeMolecule(IMolecule) - Method in class etomica.nbr.cell.molecule.CellMolecular
-
- removeMoleculeListDisplayLSMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removeMoleculeListDisplayLSMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removeMoleculeListDisplayTMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removeMoleculeListDisplayTMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removeObject(T[], T) - Static method in class etomica.util.Arrays
-
Returns an array formed by removing the given object from the given array.
- removeObjectByBox(Box) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- removeOption(String) - Method in class etomica.graphics.DeviceSelector
-
- removeParser(ParameterParser) - Method in class etomica.util.ParameterBase
-
- removePlane(Plane) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- removePotential(IPotentialMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- removePotential(IPotentialAtomic) - Method in class etomica.nbr.list.PotentialMasterList
-
- removePotential(IPotentialMolecular) - Method in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- removePotential(IPotentialAtomic) - Method in class etomica.nbr.PotentialGroupNbr
-
- removePotential(IPotentialAtomic) - Method in class etomica.nbr.PotentialMasterHybrid
-
- removePotential(IPotentialAtomic) - Method in class etomica.nbr.PotentialMasterNbr
-
- removePotential(IPotential) - Method in class etomica.potential.PotentialArray
-
Removes the given potential and the associated criterion from the list
held by this type instance, and returns the index that was assigned to
it.
- removePotential(IPotential) - Method in class etomica.potential.PotentialArrayByType
-
Removes the given potential and the associated criterion from the list
held by this type instance, and returns the index that was assigned to
it.
- removePotential(IPotentialMolecular) - Method in class etomica.potential.PotentialArrayMolecular
-
Removes the given potential and the associated criterion from the list
held by this type instance, and returns the index that was assigned to
it.
- removePotential(IPotentialAtomic) - Method in class etomica.potential.PotentialGroup
-
Removes given potential from the group.
- removePotential(IPotentialMolecular) - Method in class etomica.potential.PotentialMaster
-
Removes given potential from the group.
- removePotential(IPotentialAtomic) - Method in class etomica.potential.PotentialMaster
-
Removes given potential from the group.
- removePotential(IPotentialAtomic) - Method in class etomica.potential.PotentialMasterMonatomic
-
- removePotentialJListListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removePotentialJListListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removePotParamDisplayLSMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removePotParamDisplayLSMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removePotParamDisplayTMListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removePotParamDisplayTMListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class etomica.graphics.Display
-
- removePropertyChangeListener(PropertyChangeListener) - Method in class etomica.util.Grabber.ActionCornerSetter
-
- removeSpecies(ISpecies) - Method in class etomica.config.ConfigurationLatticeWithPlane
-
- removeSpecies(ISpecies) - Method in class etomica.simulation.Simulation
-
Removes the given ISpecies from the Simulation.
- removeSpecies() - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
-
- removeSpeciesAtIndex(int) - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
-
- removeSpeciesJListListener() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- removeSpeciesJListListener() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- removeSpeciesMolecule(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- removeSpeciesNotify(ISpecies) - Method in class etomica.box.Box
-
Notifies the Box that a Species has been removed.
- removeValueChangedListener(DeviceBoxValueChangedListener) - Method in class etomica.graphics.DeviceBox
-
Remove an object that is listening for the DeviceBox value to change
- renderAllStrings(Object) - Method in class org.jmol.g3d.Graphics3D
-
- renderAllStrings(Object) - Method in class org.jmol.util.GData
-
- renderBackground(Graphics3D) - Method in class org.jmol.g3d.Graphics3D
-
- renderBackground(Graphics3D) - Method in class org.jmol.util.GData
-
- renderCrossHairs(int[], int, int, Point3f, float) - Method in class org.jmol.g3d.Graphics3D
-
- renderHermiteRibbon(boolean, boolean, int, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, Point3i, int, int) - Method in class org.jmol.g3d.HermiteRenderer
-
- renderHermiteRope(boolean, int, int, int, int, Point3i, Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.HermiteRenderer
-
- RenderMD - Class in etomica.modules.render
-
Three-dimensional hard-sphere molecular dynamics simulation, using
neighbor listing.
- RenderMD(Space) - Constructor for class etomica.modules.render.RenderMD
-
Sole public constructor, makes a simulation using a 3D space.
- RenderMD(Space, RenderMD.RenderMDParam) - Constructor for class etomica.modules.render.RenderMD
-
- RenderMD.CriterionCar - Class in etomica.modules.render
-
- RenderMD.P2PenetrableCar - Class in etomica.modules.render
-
- RenderMD.RenderMDParam - Class in etomica.modules.render
-
Inner class for parameters understood by the HSMD3D constructor
- RenderMDGraphic - Class in etomica.modules.render
-
- RenderMDGraphic(RenderMD, Space) - Constructor for class etomica.modules.render.RenderMDGraphic
-
- RenderMDParam() - Constructor for class etomica.modules.render.RenderMD.RenderMDParam
-
- repaint() - Method in class etomica.graphics.Display
-
- repaint() - Method in class etomica.graphics.DisplayBox
-
Repaint the graphic associated with the display box.
- repaint() - Method in class etomica.graphics.DisplayCanvas
-
- repaint() - Method in class etomica.graphics.DisplayPolytope
-
- repaint() - Method in class etomica.graphics.DisplayTable
-
- repaint() - Method in class etomica.graphics.PropertyText
-
- repaint(Object) - Method in interface org.jmol.api.ApiPlatform
-
- repaint(Object) - Method in class org.jmol.awt.Platform
-
- REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
-
- REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.MultiharmonicGraphicMC
-
- REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- REPAINT_INTERVAL - Static variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
-
- repaintSleep - Variable in class etomica.graphics.SimulationGraphic
-
- repaintwaitms - Static variable in class org.jmol.script.Token
-
- replaceAllCharacter(String, String, char) - Static method in class org.jmol.util.TextFormat
-
Does a clean replace of any of the characters in str with chrTo
If strTo contains strFrom, then only a single pass is done.
- replaceAllCharacters(String, String, String) - Static method in class org.jmol.util.TextFormat
-
Does a clean replace of any of the characters in str with strTo
If strTo contains strFrom, then only a single pass is done.
- replaceQuotedStrings(Vector, Vector, String, int) - Static method in class etomica.util.ScientificFormat
-
- replaceQuotedStrings(String, List<String>, List<String>) - Static method in class org.jmol.util.TextFormat
-
- replaceStrings(String, List<String>, List<String>) - Static method in class org.jmol.util.TextFormat
-
- replicate(Configuration, Box, int[], Space) - Static method in class etomica.config.ConfigurationFileBinary
-
Reads the configuration from the file and then replicates the
configuration reps times in each direction.
- replicate(Configuration, Box, int[], Space) - Static method in class etomica.config.ConfigurationReplicate
-
Replicates the configuration from config within boxBig.
- REPULSION_ATTRACTION - Static variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- REPULSION_ONLY - Static variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- requestFocusInWindow(Object) - Method in interface org.jmol.api.ApiPlatform
-
- requestFocusInWindow(Object) - Method in class org.jmol.awt.Platform
-
- Requirement - Class in etomica.compatibility
-
- Requirement() - Constructor for class etomica.compatibility.Requirement
-
- RequirementSet - Class in etomica.compatibility
-
- rescale(Configuration, Box, double, Space) - Static method in class etomica.config.ConfigurationFileBinary
-
- rescaleBox(double) - Method in class etomica.normalmode.SimFluidSoftSphere
-
- rescaledCoords0 - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- rescalingToFitVolume - Variable in class etomica.config.ConfigurationLattice
-
- rescalingToFitVolume - Variable in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
- rescalingToFitVolume - Variable in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
- reservoir - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- reset() - Method in class etomica.action.activity.ActivityGroupSeries
-
Marks all actions as pending.
- reset() - Method in class etomica.action.activity.Controller
-
Marks all actions as pending.
- reset() - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
- reset() - Method in class etomica.atom.iterator.ANIntergroupExchange
-
- reset() - Method in class etomica.atom.iterator.ANIntragroupExchange
-
- reset() - Method in class etomica.atom.iterator.ApiIndexList
-
Resets iterator to a state where hasNext is true, if atoms in pair are
not null.
- reset() - Method in class etomica.atom.iterator.ApiInnerVariable
-
Resets the iterator, so that it is ready to go through all of its pairs.
- reset() - Method in class etomica.atom.iterator.ApiInterArrayList
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.atom.iterator.ApiIntergroup
-
- reset() - Method in class etomica.atom.iterator.ApiIntergroupCoupled
-
- reset() - Method in class etomica.atom.iterator.ApiIntergroupExchange
-
- reset() - Method in class etomica.atom.iterator.ApiIntraArrayList
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.atom.iterator.ApiIntragroup
-
Puts iterator in a state to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
- reset() - Method in class etomica.atom.iterator.AtomIteratorArrayList
-
Puts iterator in state ready to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
Readies the iterator to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Puts iterator in state ready to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorBasis
-
Puts iterator in a state ready to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart
-
Puts iterator in a state ready to begin iteration.
- reset() - Method in class etomica.atom.iterator.AtomIteratorNull
-
- reset() - Method in class etomica.atom.iterator.AtomIteratorSinglet
-
Resets iterator to a state where hasNext is true.
- reset() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
Resets iterator to a state where hasNext is true, if atoms in pair are
not null.
- reset() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
Resets iterator to a state where hasNext is true, if atoms in pair are
not null.
- reset() - Method in interface etomica.atom.iterator.AtomsetIterator
-
Resets the iterator to loop through its iterates again.
- reset() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
- reset() - Method in class etomica.atom.iterator.TripletInnerSequential
-
- reset() - Method in class etomica.config.ConformationChain
-
Resets the vector instructions.
- reset() - Method in class etomica.config.ConformationChain2D
-
- reset() - Method in class etomica.config.ConformationChain3D
-
- reset() - Method in class etomica.config.ConformationChainZigZag
-
- reset() - Method in class etomica.config.ConformationChainZigZag2
-
- reset() - Method in class etomica.data.AccumulatorAverage
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageBlockless
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageBootstrap
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageCollapsing
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorAverageCovariance
-
- reset() - Method in class etomica.data.AccumulatorAverageFixed
-
- reset() - Method in class etomica.data.AccumulatorAverageFixedOutputFile
-
Resets all sums to zero.
- reset() - Method in class etomica.data.AccumulatorCounter
-
Sets count to zero.
- reset() - Method in class etomica.data.AccumulatorHistogram
-
Zeros histograms, discarding any previous contributions.
- reset() - Method in class etomica.data.AccumulatorHistory
-
- reset() - Method in class etomica.data.AccumulatorRatioAverageCovariance
-
- reset() - Method in class etomica.data.AccumulatorRatioAverageCovarianceFull
-
- reset() - Method in class etomica.data.DataAccumulator
-
Clear accumulated values.
- reset() - Method in class etomica.data.DataArrayWriter
-
- reset() - Method in interface etomica.data.DataLogger.DataWriter
-
Informs the DataSink that it will be writing the beginning of the
file so printing header information is appropriate.
- reset() - Method in class etomica.data.DataPumpListenerPow
-
- reset() - Method in class etomica.data.DataPumpListenerPowStrict
-
- reset() - Method in class etomica.data.DataSet
-
- reset() - Method in class etomica.data.DataTableWriter
-
- reset() - Method in interface etomica.data.histogram.Histogram
-
resets all histogram values and counts to zero
- reset() - Method in class etomica.data.histogram.HistogramCollapsing
-
- reset() - Method in class etomica.data.histogram.HistogramDiscrete
-
- reset() - Method in class etomica.data.histogram.HistogramExpanding
-
- reset() - Method in class etomica.data.histogram.HistogramNotSoSimple
-
- reset() - Method in class etomica.data.histogram.HistogramReweightedData
-
- reset() - Method in class etomica.data.histogram.HistogramSimple
-
- reset() - Method in interface etomica.data.history.History
-
Resets the History.
- reset() - Method in class etomica.data.history.HistoryCollapsing
-
Removes entire history, setting all values to NaN.
- reset() - Method in class etomica.data.history.HistoryCollapsingAverage
-
- reset() - Method in class etomica.data.history.HistoryComplete
-
Removes entire history, setting all values to NaN.
- reset() - Method in class etomica.data.history.HistoryScrolling
-
Removes entire history, setting all values to NaN.
- reset() - Method in class etomica.data.meter.MeterDihedralAngle
-
Zero's out the G(phi) sum tracked by this meter.
- reset() - Method in class etomica.data.meter.MeterMeanSquareDisplacement
-
Specifies the set of atoms that will be tracked to compute their MSD.
- reset() - Method in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
-
- reset() - Method in class etomica.data.meter.MeterPressureHard
-
- reset() - Method in class etomica.data.meter.MeterProfile
-
- reset() - Method in class etomica.data.meter.MeterProfileByAtoms
-
- reset() - Method in class etomica.data.meter.MeterProfileByVolume
-
- reset() - Method in class etomica.data.meter.MeterRDF
-
Zero's out the RDF sum tracked by this meter.
- reset() - Method in class etomica.data.meter.MeterRDFPC
-
Zero's out the RDF sum tracked by this meter.
- reset() - Method in class etomica.data.meter.PotentialCalculationRDF
-
Zero's out the RDF sum tracked by this meter.
- reset() - Method in class etomica.dimer.IntegratorDimerMin
-
- reset() - Method in class etomica.dimer.IntegratorDimerRT
-
- reset() - Method in class etomica.dimer.PotentialCalculationForcePressureSumGB
-
Zeros out the pressureTensor.
- reset() - Method in class etomica.freeenergy.npath.PotentialCalculationDUDW
-
- reset() - Method in class etomica.graphics.DeviceControllerButton
-
Sets label of button to display "Start".
- reset() - Method in class etomica.graphics.DeviceTrioControllerButton
-
Sets controller toggle button to read "Start"
- reset() - Method in class etomica.integrator.Integrator
-
Defines the actions taken by the integrator to reset itself, such as
required if a perturbation is applied to the simulated box (e.g.,
addition or deletion of a molecule).
- reset() - Method in class etomica.integrator.IntegratorBox
-
Performs superclass reset actions and recalculated currentPotentialEnergy
- reset() - Method in class etomica.integrator.IntegratorGear4
-
- reset() - Method in class etomica.integrator.IntegratorGear4NPH
-
- reset() - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp
-
resets the "atom" held by this class, ensuring the method will
work even if (coincidentally) the atom is the same as the same
one as the last time the method was called.
- reset() - Method in class etomica.integrator.IntegratorHard
-
- reset() - Method in class etomica.integrator.IntegratorManagerMC
-
Causes recalculation of move frequencies and zero of selection counts for
moves.
- reset() - Method in class etomica.integrator.IntegratorMC
-
Causes recalculation of move frequencies and zero of selection counts for
moves.
- reset() - Method in class etomica.integrator.IntegratorMD
-
- reset() - Method in class etomica.integrator.IntegratorRigidIterative
-
- reset() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- reset() - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- reset() - Method in class etomica.integrator.IntegratorVelocityVerletRattle
-
- reset() - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- reset() - Method in class etomica.integrator.IntegratorVerlet
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- reset() - Method in class etomica.integrator.mcmove.MCMoveTracker
-
- reset() - Method in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
-
Re-zeros the force vector.
- reset() - Method in class etomica.lattice.CellLattice.NeighborIterator
-
- reset() - Method in interface etomica.lattice.IndexIterator
-
- reset() - Method in class etomica.lattice.IndexIteratorIncreasing
-
Resets the iterator.
- reset() - Method in class etomica.lattice.IndexIteratorRectangular
-
Puts iterator in a condition to begin iteration.
- reset() - Method in class etomica.lattice.IndexIteratorReflecting
-
- reset() - Method in class etomica.lattice.IndexIteratorTriangular
-
Sets iterator to begin returning iterates.
- reset() - Method in class etomica.lattice.IndexIteratorTriangularPermutations
-
- reset() - Method in class etomica.lattice.RectangularLattice.Iterator
-
- reset() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Resets the iterator to loop through its iterates again.
- reset() - Method in interface etomica.lattice.SiteIterator
-
Puts the iterator in a state ready to begin iteration.
- reset() - Method in class etomica.mappedRdf.MeterMappedRdf
-
Zero's out the RDF sum tracked by this meter.
- reset() - Method in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- reset() - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- reset() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- reset() - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- reset() - Method in class etomica.math.discrete.CombinationIterator
-
- reset() - Method in class etomica.math.discrete.FixedSumIterator
-
Sets the iterator to begin iteration.
- reset() - Method in class etomica.math.discrete.PermutationDegenerateIterator
-
Readies the iterator for iteration.
- reset() - Method in class etomica.math.discrete.PermutationIterator
-
- reset() - Method in class etomica.meam.P2EAM
-
- reset() - Method in class etomica.metastable.MeterDensityDistribution
-
- reset() - Method in class etomica.models.nitrogen.MeterNormalizedCoord
-
Sets the tensor summation to 0.
- reset() - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta
-
Sets the tensor summation to 0.
- reset() - Method in class etomica.models.nitrogen.MeterOrientationDistribution
-
Sets the tensor summation to 0.
- reset() - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup
-
Sets the tensor summation to 0.
- reset() - Method in class etomica.modules.adsorption.EOSSW
-
- reset() - Method in class etomica.modules.adsorption.EOSSWPatel
-
- reset() - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- reset() - Method in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
-
- reset() - Method in class etomica.modules.adsorption.ModifierPMu
-
- reset() - Method in class etomica.modules.adsorption.VEOS3SW
-
- reset() - Method in class etomica.modules.catalysis.InteractionTracker
-
- reset() - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- reset(IAtom) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
-
- reset() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- reset() - Method in class etomica.modules.droplet.IntegratorDroplet
-
- reset() - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- reset() - Method in class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- reset() - Method in class etomica.modules.joulethomson.IntegratorJT
-
- reset() - Method in class etomica.modules.materialfracture.PotentialCalculationForceStress
-
- reset() - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- reset() - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
Resets all sums to zero
- reset() - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- reset() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
-
- reset() - Method in class etomica.modules.pistoncylinder.MeterRDFCylinder
-
- reset(IAtom) - Method in class etomica.modules.render.RenderMD.CriterionCar
-
- reset() - Method in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
-
Re-zeros the force vectors.
- reset() - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
Re-zeros the force vectors.
- reset(IAtom) - Method in class etomica.modules.sam.CriterionTether3
-
- reset() - Method in class etomica.modules.sam.PotentialCalculationForceSumWall
-
- reset() - Method in class etomica.modules.vle.B2Fit.FunctionMayerB2LJQ
-
- reset() - Method in class etomica.molecule.iterator.MoleculeIteratorAll
-
- reset() - Method in class etomica.molecule.iterator.MoleculeIteratorArrayList
-
Puts iterator in state ready to begin iteration.
- reset() - Method in class etomica.molecule.iterator.MoleculeIteratorArrayListSimple
-
Puts iterator in state ready to begin iteration.
- reset() - Method in class etomica.molecule.iterator.MoleculeIteratorMolecule
-
- reset() - Method in class etomica.molecule.iterator.MoleculeIteratorSinglet
-
Resets iterator to a state where hasNext is true.
- reset() - Method in class etomica.molecule.iterator.MpiInnerFixed
-
Resets the iterator, so that it is ready to go through all of its pairs.
- reset() - Method in class etomica.molecule.iterator.MpiInnerVariable
-
Resets the iterator, so that it is ready to go through all of its pairs.
- reset() - Method in class etomica.molecule.iterator.MpiInterArrayList
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.molecule.iterator.MpiInterspecies1A
-
- reset() - Method in class etomica.molecule.iterator.MpiInterspeciesAA
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.molecule.iterator.MpiIntraArrayList
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.molecule.iterator.MpiIntraspecies1A
-
- reset() - Method in class etomica.molecule.iterator.MpiIntraspeciesAA
-
Sets iterator in condition to begin iteration.
- reset() - Method in class etomica.molecule.iterator.MpiMolecule
-
Readies iterator for iteration.
- reset() - Method in class etomica.nbr.cell.Api1ACell
-
- reset() - Method in class etomica.nbr.cell.ApiAACell
-
- reset() - Method in class etomica.nbr.cell.AtomIteratorCell
-
- reset() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
- reset() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
- reset() - Method in class etomica.nbr.cell.molecule.MpiAACell
-
- reset() - Method in class etomica.nbr.cell.PotentialMasterCell
-
Reassign atoms to cell lists for all boxes.
- reset(IAtom) - Method in class etomica.nbr.CriterionAdapter
-
Indicates to wrapped criterion that given atom's neighbor list has just
been updated, and that properties (e.g., record of atom's position) used
by needUpdate and unsafe() methods should be reset.
- reset(IAtom) - Method in class etomica.nbr.CriterionAll
-
Performs no action.
- reset(IAtom) - Method in class etomica.nbr.CriterionNone
-
Performs no action.
- reset(IAtom) - Method in class etomica.nbr.CriterionPositionWall
-
- reset(IAtom) - Method in class etomica.nbr.CriterionSimple
-
- reset() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
For each box in the array, applies central image,
resets neighbors of all atoms, and sets up all neighbor
lists.
- reset() - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Recomputes the maximum potential range (which might change without this
class receiving notification) and readjust cell lists
- reset() - Method in class etomica.nbr.list.NeighborListManager
-
For each box in the array, applies central image,
resets neighbors of all atoms, and sets up all neighbor
lists.
- reset() - Method in class etomica.nbr.list.PotentialMasterList
-
Recomputes the maximum potential range (which might change without this
class receiving notification) and readjust cell lists
- reset(IMolecule) - Method in class etomica.nbr.molecule.CriterionAdapterMolecular
-
Indicates to wrapped criterion that given atom's neighbor list has just
been updated, and that properties (e.g., record of atom's position) used
by needUpdate and unsafe() methods should be reset.
- reset(IMolecule) - Method in class etomica.nbr.molecule.CriterionAllMolecular
-
Performs no action.
- reset(IMolecule) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- reset(IMolecule) - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular
-
Indicates to criterion that given molecule's neighbor list has just been
updated, and that properties (e.g., record of molecule's position)
used by needUpdate and unsafe() methods should be reset.
- reset(IAtom) - Method in interface etomica.nbr.NeighborCriterion
-
Indicates to criterion that given atom's neighbor list has just been
updated, and that properties (e.g., record of atom's position)
used by needUpdate and unsafe() methods should be reset.
- reset() - Method in class etomica.nbr.site.Api1ASite
-
- reset() - Method in class etomica.normalmode.HSNPT.ActionSummer
-
- reset() - Method in class etomica.normalmode.IntegratorHardMDMC
-
- reset() - Method in class etomica.normalmode.MeterNormalMode
-
Sets the tensor summation to 0.
- reset() - Method in class etomica.normalmode.MeterTiltHistogram
-
- reset() - Method in class etomica.normalmode.MeterTiltRotationHistogram
-
- reset() - Method in class etomica.normalmode.PotentialCalculationEFSSP
-
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
- reset() - Method in class etomica.normalmode.PotentialCalculationLJSP
-
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
- reset() - Method in class etomica.overlap.IntegratorOverlap
-
- reset() - Method in class etomica.potential.PotentialCalculationForcePressureSum
-
Zeros out the pressureTensor.
- reset() - Method in class etomica.potential.PotentialCalculationForceSum
-
Re-zeros the force vectors.
- reset() - Method in class etomica.potential.PotentialCalculationTorqueSum
-
Re-zeros the force vectors.
- reset() - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- reset() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- reset() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- reset() - Method in interface etomica.space.RotationTensor
-
Sets tensor to a condition of no rotation.
- reset() - Method in class etomica.space1d.RotationTensor1D
-
- reset() - Method in class etomica.space2d.RotationTensor2D
-
- reset() - Method in class etomica.space3d.RotationTensor3D
-
- reset() - Method in class etomica.thermointegration.IntegratorThermodynamic
-
Resets this integrator and passes on the reset to the subIntegrator.
- reset() - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- reset() - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- reset() - Method in class etomica.util.TreeList
-
clear the tree by disconnecting everything from the head.
- reset() - Method in class etomica.virial.cluster.ClusterDiagram
-
Resets the cluster to being fully connected except that root points
are not connected to each other.
- reset() - Method in class etomica.virial.cluster.ClusterGenerator
-
Resets the cluster generator.
- reset() - Method in class etomica.virial.cluster.PermutationIterator
-
- reset(long) - Method in class etomica.virial.CoordinatePairLeafSet
-
- reset(long) - Method in class etomica.virial.CoordinatePairMoleculeSet
-
- reset(long) - Method in interface etomica.virial.CoordinatePairSet
-
Informs the CoordinatePairSet that the configuration has changed and that it
has a new ID
- reset() - Method in class etomica.virial.GUI.models.ModelAlkaneLengthSelection
-
- reset() - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
Reset to initial value.
- reset() - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- reset() - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- reset() - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
-
- reset() - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- reset() - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- reset() - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
Resets all sums to zero
- reset() - Method in class etomica.virial.overlap.DataSourceVirialOverlap
-
Convenience method that resets reference and target accumulators
- reset() - Method in class etomica.virial.overlap.DataVirialOverlap
-
Convenience method that resets reference and target accumulators
- reset() - Method in class etomica.virial.overlap.IntegratorOverlap
-
- reset() - Method in interface g3dsys.control.IndexIterator
-
Resets iteration; should be called before use
- reset() - Method in class org.jmol.util.BoxInfo
-
- resetAcceptance() - Method in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- ResetAccumulators - Class in etomica.action
-
- ResetAccumulators() - Constructor for class etomica.action.ResetAccumulators
-
- ResetAccumulatorsAveraged - Class in etomica.action
-
- ResetAccumulatorsAveraged() - Constructor for class etomica.action.ResetAccumulatorsAveraged
-
- resetAction - Variable in class etomica.graphics.DeviceNSelector
-
- resetAction - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
-
- resetAction - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- resetAdjustStep() - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
Resets damped step adjustment.
- resetAxes() - Method in class etomica.graphics.EtomicaPlot
-
Overrides a not-so-useful method in superclass
- resetBonds() - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- resetBonds() - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- resetCollision() - Method in class etomica.integrator.IntegratorHard.Agent
-
resets collision potential and partner.
- resetCollisionFull() - Method in class etomica.integrator.IntegratorHard.Agent
-
resets time, potential and partner.
- resetCollisionTimes() - Method in class etomica.integrator.IntegratorHard
-
Do an upList call for each atom and reconstruct the event list.
- resetData() - Method in class etomica.data.meter.MeterStructureFactor
-
- resetFilter() - Method in interface etomica.atom.AtomFilterCollective
-
Informs the filter that something in the system has changed (atom
positions, velocityies, etc) has changed and the filtered status of the
atoms should be determined.
- resetFilter() - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- resetFilter() - Method in class etomica.modules.droplet.AtomFilterLiquid
-
- resetFilter() - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- resetHybridAcceptance() - Method in class etomica.integrator.IntegratorMD
-
Zeros counters used to track acceptance fraction of HYBRID_MC thermostat.
- resetNewMoleculePair() - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- resetNewMoleculePair() - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- resetPiston() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
-
- resetRotation() - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
- resetScale() - Method in class etomica.graphics.DisplayScrollingGraph
-
- resetSelectionViewANew() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- resetSlab() - Method in class org.jmol.util.MeshSurface
-
- resetStepCount() - Method in class etomica.integrator.Integrator
-
This method resets the step counter.
- resetStepCount() - Method in class etomica.integrator.IntegratorMD
-
- resetStepCount() - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- resetViewAfterSSSPException() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- resetViewToDisplaySpecies1() - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- reshape(int, int) - Method in class etomica.graphics.DisplayCanvas
-
Same as setSize, but included to implement DisplayCanvasInterface,
which has this for compatibility with OpenGL.
- residual - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- residue - Static variable in class org.jmol.script.Token
-
- resizeData(int) - Method in class etomica.data.AccumulatorAverageBootstrap
-
- resizeData(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
- resizeData(int) - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
-
- resizeDimer() - Method in class etomica.dimer.IntegratorDimerRT
-
- resizeGraphic() - Method in class etomica.graphics.DevicePlotPoints
-
Returns the top level panel that the plot scale resizing components sit on.
- resno - Static variable in class org.jmol.script.Token
-
- RESOURCES - Static variable in class etomica.graph.view.rasterizer.Messages
-
The error messages bundle class name.
- restartAction - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- resume - Static variable in class org.jmol.script.Token
-
- retainAll(Collection<?>) - Method in class etomica.graph.model.GraphList
-
- returnMu - Variable in class etomica.normalmode.DataSourcePMu
-
- ReturnValue(int, Space) - Constructor for class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
-
- reverse(double[], double) - Static method in class etomica.math.numerical.SineTransform
-
- reverse - Static variable in class org.jmol.script.Token
-
- reverseCollisionHandler - Variable in class etomica.integrator.IntegratorHard
-
- ReverseOsmosis - Class in etomica.modules.rosmosis
-
Reverse osmosis simulation, based on simulation code by Sohail Murad.
- ReverseOsmosis(Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosis
-
- ReverseOsmosisGraphic - Class in etomica.modules.rosmosis
-
Graphical and data collection bits for reverse osmosis simulation.
- ReverseOsmosisGraphic(ReverseOsmosis, Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- ReverseOsmosisGraphic.Applet - Class in etomica.modules.rosmosis
-
- ReverseOsmosisGraphic.DataSinkExcludeOverlap - Class in etomica.modules.rosmosis
-
- ReverseOsmosisGraphic.ModifierAtomDiameter - Class in etomica.modules.rosmosis
-
- ReverseOsmosisGraphic.ModifierEpsilon - Class in etomica.modules.rosmosis
-
- ReverseOsmosisWater - Class in etomica.modules.rosmosis
-
Reverse osmosis simulation, based on simulation code by Sohail Murad.
- ReverseOsmosisWater(Space) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWater
-
- ReverseOsmosisWaterGraphic - Class in etomica.modules.rosmosis
-
Graphical and data collection bits for reverse osmosis simulation.
- ReverseOsmosisWaterGraphic(ReverseOsmosisWater) - Constructor for class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- ReverseOsmosisWaterGraphic.Applet - Class in etomica.modules.rosmosis
-
- ReverseOsmosisWaterGraphic.DataSinkExcludeOverlap - Class in etomica.modules.rosmosis
-
- ReverseOsmosisWaterGraphic.ModifierAtomDiameter - Class in etomica.modules.rosmosis
-
- ReverseOsmosisWaterGraphic.ModifierEpsilon - Class in etomica.modules.rosmosis
-
- ReverseOsmosisWaterGraphic.ModifierSoluteCharge - Class in etomica.modules.rosmosis
-
- revertDiagram() - Method in class etomica.virial.ClusterSumStickyEF
-
set the diagram used for calculating the value to the ith diagram.
- revertF() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- revertF() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- revertF() - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- revertF() - Method in class etomica.virial.ClusterTree
-
- rewind - Static variable in class org.jmol.script.Token
-
- rFill(StringXBuilder, String, String) - Static method in class org.jmol.util.TextFormat
-
- rfit - Static variable in class etomica.potential.P2O2Bartolomei
-
- rfit0 - Static variable in class etomica.potential.P2O2Bartolomei
-
- rfitMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- rfitPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- rg - Variable in class etomica.modules.droplet.MeterDeformation
-
- rgb(int, int, int) - Static method in class org.jmol.util.ColorUtil
-
- Rgb16 - Class in org.jmol.util
-
- Rgb16() - Constructor for class org.jmol.util.Rgb16
-
- RheologyGraphic - Class in etomica.modules.rheology
-
Module for "Macromolecular dynamics related to rheological properties
through Brownian dynamics simulations", designed by Lewis Wedgewood.
- RheologyGraphic(SimulationRheology) - Constructor for class etomica.modules.rheology.RheologyGraphic
-
- RheologyGraphic.Applet - Class in etomica.modules.rheology
-
- rho - Variable in class etomica.math.numerical.VirialOptimizer
-
- rho - Variable in class etomica.meam.P2EAM
-
- rho - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
-
- rho - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
-
- rho - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
-
- rho - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- rho - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- rho - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- rho - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- rho - Variable in class etomica.virial.cluster.VirialDiagrams
-
- rho - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- rho - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rho - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rho0 - Variable in class etomica.meam.ParameterSetMEAM
-
- rho0 - Static variable in class etomica.statmech.HardSphereSolid
-
- rho0 - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rho0 - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
-
- rho0point - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
-
- rho1 - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoA - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
-
- rhoA - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoA - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- rhoA - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- rhoA - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- rhoA - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rhoA - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoAB - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
-
- rhoAB - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoAB - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- rhoAB - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rhoAB - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoAB0 - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rhoABC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoABC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoAC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoAC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoAlphaTrans - Variable in class etomica.models.nitrogen.FindTransitionTemperature
-
- rhoB - Variable in class etomica.graph.operations.DecorateWertheim2SiteRho.DecorateWertheimParameters2Site
-
- rhoB - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoB - Variable in class etomica.graph.operations.DecorateWertheimNaphthalene2Rho.DecorateNaphthalene2Site
-
- rhoB - Variable in class etomica.virial.cluster.VirialDiagramsMix
-
- rhoB - Variable in class etomica.virial.cluster.VirialDiagramsMix2
-
- rhoB - Variable in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- rhoB - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoBC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoBC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoBetaTrans - Variable in class etomica.models.nitrogen.FindTransitionTemperature
-
- rhoC - Variable in class etomica.graph.operations.DecorateWertheim3SiteRho.DecorateWertheimParameters3Site
-
- rhoc - Static variable in class etomica.modules.adsorption.EOSSW
-
- rhoC - Variable in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- rhoForPressure(double) - Method in class etomica.modules.adsorption.EOSSW
-
- rhoForPressure(double) - Method in class etomica.modules.adsorption.EOSSWPatel
-
- rhoForPressure(double) - Method in class etomica.modules.adsorption.VEOS3SW
-
- rhograd - Variable in class etomica.meam.P2EAM
-
- rhograd - Variable in class etomica.meam.PotentialCuLREP
-
- rhograd - Variable in class etomica.meam.PotentialEAM
-
- rhograd - Variable in class etomica.meam.PotentialEAM_LS
-
- rhograd - Variable in class etomica.meam.PotentialEFS
-
- rhoi(IAtomList) - Method in class etomica.meam.PotentialMEAM
-
- rhoi1sq() - Method in class etomica.meam.PotentialMEAM
-
- rhoi2sq() - Method in class etomica.meam.PotentialMEAM
-
- rhoi3sq() - Method in class etomica.meam.PotentialMEAM
-
- RHOj0 - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj1x - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj1y - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj1z - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2 - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2xx - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2xy - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2xz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2yy - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2yz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj2zz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xxx - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xxy - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xxz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xyy - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xyz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3xzz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3yyy - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3yyz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3yzz - Static variable in class etomica.meam.PotentialMEAM
-
- RHOj3zzz - Static variable in class etomica.meam.PotentialMEAM
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
-
- rhopoint - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
-
- rHSCore - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- ri - Variable in class etomica.models.co2.P2CO2Hellmann
-
- ri - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- ri - Variable in class etomica.potential.P3Induction
-
- ribbon - Static variable in class org.jmol.script.Token
-
- ribbonaspectratio - Static variable in class org.jmol.script.Token
-
- ribbonborder - Static variable in class org.jmol.script.Token
-
- RIGHT - Static variable in class etomica.graphics.DisplayBox
-
- RIGHT - Static variable in class etomica.graphics.DisplayPolytope
-
- right - Static variable in class org.jmol.script.Token
-
- rightAngle - Static variable in class etomica.lattice.crystal.Primitive
-
- rightDifference(Quaternion) - Method in class org.jmol.util.Quaternion
-
- rij - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- rij - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- rij - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- Rij - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- rij - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- Rij - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- rij - Variable in class etomica.potential.P3Induction
-
- rijVector - Variable in class etomica.models.co2.PNCO2GCPM
-
- rijVector - Variable in class etomica.models.co2.PNGCPM
-
- rijVector - Variable in class etomica.models.water.PNWaterGCPM
-
- rik - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- rik - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- rik - Variable in class etomica.potential.P3Induction
-
- rIndices - Variable in class etomica.virial.cluster.PermutationIterator
-
- Ring - Class in etomica.virial.cluster
-
- Ring(int) - Constructor for class etomica.virial.cluster.Ring
-
Constructor for Ring.
- ring(int) - Static method in class etomica.virial.cluster.Standard
-
Returns a ring of bonds, {{0,1},{1,2},...{n-2,n-1},{n-1,0}}
- ring0 - Variable in class etomica.virial.simulations.ModifierTPI
-
- ring1 - Variable in class etomica.virial.simulations.ModifierTPI
-
- RING_CHAIN_TREES - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- RING_CHAIN_TREES - Static variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- RING_CHAIN_TREES - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- RING_CHAIN_TREES - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- RING_TREE - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- RING_TREE - Static variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- RING_TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- RING_TREE - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- ringFrac - Variable in class etomica.virial.ClusterChainHS
-
- ringFrac - Variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- ringFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- ringFrac - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- ringFrac - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- ringFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- ringFrac - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- ringFrac - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- ringHS(int) - Static method in class etomica.virial.cluster.Standard
-
Return integral for ring of hard spheres of size nPoints
- ringResult - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
- RingResult() - Constructor for class etomica.modules.chainequilibrium.P2SquareWellBonded.RingResult
-
- rings - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- RINGS - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- RINGS - Static variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- RINGS - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- RINGS - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- rj - Variable in class etomica.models.co2.P2CO2Hellmann
-
- rj - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rj - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- rj - Variable in class etomica.potential.P3Induction
-
- rjk - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- rjk - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- rjrj - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- rk - Variable in class etomica.potential.P3Induction
-
- rkl - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- rLast - Variable in class etomica.data.meter.MeterMeanSquareDisplacement
-
- rm() - Method in class etomica.atom.AtomType
-
- rm() - Method in class etomica.chem.elements.Element
-
- rm - Variable in class etomica.chem.elements.ElementChemical
-
- rm() - Method in class etomica.chem.elements.ElementChemical
-
- rm - Variable in class etomica.chem.elements.ElementSimple
-
- rm() - Method in class etomica.chem.elements.ElementSimple
-
- rm() - Method in interface etomica.chem.elements.IElement
-
- rMax - Variable in class etomica.data.meter.MeterDihedralAngle
-
- rMax - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- rmax - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
-
- rMaxSafe - Variable in class etomica.nbr.CriterionPositionWall
-
- rMin - Variable in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- rMin - Static variable in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- rMin - Static variable in class etomica.potential.P2HydrogenPatkowski
-
- rMin - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- rMin - Static variable in class etomica.potential.P2O2Bartolomei
-
- rMrLast - Variable in class etomica.integrator.IntegratorVerlet.Agent
-
- rmsdFile - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- rna - Static variable in class org.jmol.script.Token
-
- rNbr - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- rocket - Static variable in class org.jmol.script.Token
-
- rocketbarrels - Static variable in class org.jmol.script.Token
-
- rOM - Static variable in class etomica.models.water.ConformationWaterTIP4P
-
- root(int, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The integer root.
- root(int) - Method in class etomica.veos.bigdecimal.Ifactor
-
Pulling the r-th root.
- root(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
r-th root.
- rootD(double) - Method in class etomica.space.Space
-
- rootD(double) - Method in class etomica.space1d.Space1D
-
- rootD(double) - Method in class etomica.space2d.Space2D
-
Returns the square root of the given value, a^(1/D), which is a^(1/2).
- rootD(double) - Method in class etomica.space3d.Space3D
-
Returns the cube root of the given value, a^(1/D) which is a^(1/3).
- rootDeg(BigInteger) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Compute the order of the root r.
- rootPointsSpecial - Static variable in class etomica.graph.model.impl.MetadataImpl
-
- rot - Variable in class etomica.models.hexane.TestHexane
-
- rot - Variable in class etomica.models.hexane.TestHexaneFileConfig
-
- rot - Variable in class etomica.models.hexane.TestHexaneHarmonic
-
- rot - Variable in class etomica.models.hexane.TestSetToUHexane
-
- rot - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rot0 - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- rot0 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rot0 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rot1 - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- rot1 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rot1 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rotate - Variable in class etomica.dimer.IntegratorDimerMin
-
- rotate - Variable in class etomica.dimer.IntegratorDimerRT
-
- rotate - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- rotate - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- rotate - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- rotate - Static variable in class org.jmol.script.Token
-
- rotate(Matrix4f) - Method in class org.jmol.util.Quadric
-
- rotateBy(double, double, Vector, Vector) - Static method in class etomica.potential.P2NitrogenHellmann
-
- rotateBy(double) - Method in interface etomica.space2d.IOrientation2D
-
Rotate the orientation by the amount dt (radians) in the
counter-clockwise direction.
- rotateBy(double) - Method in class etomica.space2d.Orientation2D
-
Rotates orientation around the given axis by the given value.
- rotateBy(double, Vector) - Method in interface etomica.space3d.IOrientation3D
-
Rotate the orientation by the amount dt (radians) about the given axis.
- rotateBy(double, Vector) - Method in class etomica.space3d.Orientation3D
-
Rotates orientation by the given value about the given axis.
- rotateBy(double, Vector) - Method in class etomica.space3d.OrientationFull3D
-
Rotates orientation by the given value about the given axis.
- rotateByX(float) - Method in class g3dsys.control.G3DSys
-
Rotate the display around the x axis
- rotateByXY(float, float) - Method in class g3dsys.control.G3DSys
-
Rotate the display around the x and y axes
- rotateByY(float) - Method in class g3dsys.control.G3DSys
-
Rotate the display around the y axis
- rotateByZ(float) - Method in class g3dsys.control.G3DSys
-
Rotate the display around the z axis
- rotateDimerNewton() - Method in class etomica.dimer.IntegratorDimerMin
-
Rotates the dimer in potential energy hyperspace and aligns it with the surface's lowest
curvature mode.
- rotateDimerNewton() - Method in class etomica.dimer.IntegratorDimerRT
-
Rotates the dimer in potential energy hyperspace and aligns it with the surface's lowest
curvature mode.
- rotateMolecule - Variable in class etomica.AlkaneEH.CH4NVT
-
- rotateMolecule - Variable in class etomica.AlkaneEH.DHS_NVT
-
- rotateMolecule - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
-
- rotateMolecule - Variable in class etomica.dielectric.DHS_NVT
-
- rotateMolecule - Variable in class etomica.dielectric.DLJ_NVT_1site
-
- rotateMolecule - Variable in class etomica.dielectric.TIP4P_NVT
-
- rotateOrientation(OrientationFull3D) - Method in class etomica.math.Quaternion
-
Rotates the input orientation by using the Quaternion rotation operator L(v) = qvq*.
- rotatePhi - Variable in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- rotateTensor - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- rotateTensor - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- rotateToHome() - Method in class g3dsys.control.G3DSys
-
Remove all rotation (and translation) and return to the home position
- rotateToX(float) - Method in class g3dsys.control.TransformManager
-
- rotateToY(float) - Method in class g3dsys.control.TransformManager
-
- rotateToZ(float) - Method in class g3dsys.control.TransformManager
-
- rotateVector(Vector) - Method in class etomica.math.Quaternion
-
Rotates the input vector by using the Quaternion rotation operator L(v) = qvq*.
- rotation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- rotation - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- rotation - Variable in class etomica.models.nitrogen.TestRotationVector
-
- rotation - Static variable in class org.jmol.script.Token
-
- rotationAxis - Variable in class etomica.models.nitrogen.FindBetaN2AngleFromParameter
-
- rotationAxis - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- rotationAxis - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- rotationAxis - Variable in class etomica.models.nitrogen.TestRotationVector
-
- rotationAxis - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- rotationAxis - Variable in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- rotationL - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- rotationM - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- rotationN - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- rotationradius - Static variable in class org.jmol.script.Token
-
- rotationTensor - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- rotationTensor - Variable in class etomica.association.BiasVolumeAceticAcid
-
- rotationTensor - Variable in class etomica.association.MCMoveBiasUBMolecule
-
- rotationTensor - Variable in class etomica.association.MCMoveDimerRotate
-
- rotationTensor - Variable in class etomica.association.MCMoveSmerRotate
-
- rotationTensor - Variable in class etomica.data.meter.MeterKineticEnergyRigid
-
- rotationTensor - Variable in class etomica.integrator.IntegratorRigidIterative
-
- rotationTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- rotationTensor - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- rotationTensor - Variable in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- rotationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- rotationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- rotationTensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- rotationTensor - Variable in class etomica.models.water.OrientationCalcWater3P
-
- rotationTensor - Variable in class etomica.models.water.OrientationCalcWater4P
-
- rotationTensor - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- rotationTensor - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- RotationTensor - Interface in etomica.space
-
A tensor intended for use to perform rotations in space.
- rotationTensor - Variable in class etomica.space3d.OrientationFull3D
-
- RotationTensor1D - Class in etomica.space1d
-
Rotation tensor in 1D either flips orientation or keeps it unchanged.
- RotationTensor1D() - Constructor for class etomica.space1d.RotationTensor1D
-
Default is identity tensor that performs no rotation (flip).
- RotationTensor2D - Class in etomica.space2d
-
- RotationTensor2D() - Constructor for class etomica.space2d.RotationTensor2D
-
- rotationTensor3D - Variable in class etomica.models.water.P2Water4PSoft
-
- RotationTensor3D - Class in etomica.space3d
-
- RotationTensor3D() - Constructor for class etomica.space3d.RotationTensor3D
-
- rotationTolerance - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- rotCounter - Variable in class etomica.dimer.IntegratorDimerMin
-
- rotCounter - Variable in class etomica.dimer.IntegratorDimerRT
-
- rotDim - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- rotNum - Variable in class etomica.dimer.IntegratorDimerRT
-
- rotX(float) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to a rotation matrix about the x axis by the
passed angle.
- rotX(float) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to a rotation matrix about the x axis by the
passed angle.
- rotY(float) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to a rotation matrix about the y axis by the
passed angle.
- rotY(float) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to a rotation matrix about the y axis by the
passed angle.
- rotZ(float) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to a rotation matrix about the z axis by the
passed angle.
- rotZ(float) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to a rotation matrix about the z axis by the
passed angle.
- round(double) - Static method in class etomica.math.numerical.FastFourierTransform
-
- roundInt(int) - Static method in class org.jmol.util.GData
-
JavaScript won't really have an integer here after integer division.
- route - Variable in class etomica.action.IntegratorDimerApproach
-
- routeParams - Variable in class etomica.action.IntegratorDimerApproach
-
- rowHeaders - Variable in class etomica.data.types.DataTable.DataInfoTable
-
- rowHeaders - Variable in class etomica.data.types.DataTable.DataInfoTableFactory
-
- rowLabelColumnHeader - Variable in class etomica.graphics.DisplayTable
-
- rowLabels - Variable in class etomica.graphics.DisplayTable
-
- rp - Variable in class etomica.modules.droplet.IntegratorDroplet.MyAgent
-
- rPermutations - Variable in class etomica.virial.ClusterBonds
-
- Rpol - Variable in class etomica.models.water.P2WaterSzalewicz
-
- Rpow - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Rpow - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- Rpow - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- rPow - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
-
- rPow - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
-
- rPow - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- rPow - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
-
- rr - Variable in class etomica.potential.P2HydrogenPatkowski
-
- rr - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- rr0Tensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- rr0Tensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rr0Tensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rr0Tensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rr1Tensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- rr1Tensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rr1Tensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rr1Tensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rRand - Variable in class etomica.normalmode.MCMoveHarmonic
-
- rrlong - Variable in class etomica.potential.P2HydrogenPatkowski
-
- rrlong - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- rrounded - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
-
- rScale - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
-
- rScale - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- rScaled - Variable in class org.jmol.util.Rgb16
-
- rTensor0 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- rTensor0 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rTensor0 - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rTensor0 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rTensor1 - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- rTensor1 - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- rTensor1 - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- rTensor1 - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- rTmp - Variable in class etomica.models.water.P2WaterSzalewicz
-
- rTrial - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- rTrial - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- rTrial - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- run() - Method in class etomica.action.activity.ActivityGroupParallel
-
- run() - Method in class etomica.action.activity.ActivityGroupSeries
-
Causes uncompleted actions added to this group to be run in sequence.
- run() - Method in class etomica.action.activity.ActivityIntegrate
-
Main loop for conduct of integration.
- run() - Method in class etomica.action.activity.Controller
-
Causes uncompleted actions added to this group to be run in sequence.
- run() - Method in class etomica.action.Activity
-
Method defining the behavior of the activity.
- run(Parser.CommandValue) - Method in class etomica.graph.engine.Interpreter
-
- run() - Method in class etomica.graph.engine.Launcher.ConsoleWindowRunnable
-
- run(EtomicaServerConfig, Environment) - Method in class etomica.server.EtomicaServer
-
- run() - Method in class etomica.threaded.atom.PotentialMasterListWorker
-
- run() - Method in class etomica.threaded.domain.PotentialMasterListWorker
-
- run() - Method in class etomica.threads.ThreadsMD
-
- run() - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
-
- run() - Method in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- run() - Method in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- runBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- runBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- runBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- runBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- runBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- runEmul() - Method in class etomica.potential.PotentialEmul
-
- runGraphic(SimulationVirialOverlap2, int, DisplayTextBox, DisplayTextBox, IAction) - Method in class etomica.virial.GUI.components.SimulationRunner
-
- runit() - Method in class etomica.models.hexane.TestSetToUHexane
-
- runMD() - Method in class etomica.threads.AtomDecompositionMD
-
- runName - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- runName - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- runName - Variable in class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
-
- runName - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- runName - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- runName - Variable in class etomica.virial.simulations.VirialSQWRecalcSmallMem.VirialHSParam
-
- running - Variable in class etomica.modules.clustergenerator.MyApplet
-
- runQChem() - Method in class etomica.potential.P2QChem
-
- runSimulation(ModelSimulationEnvironment, ArrayList<ICollectionPotential>) - Method in class etomica.virial.GUI.components.SimulationRunner
-
- runVirial(VirialExternalFieldConfinedOverlap.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap
-
- runVirial(VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho
-
- runVirial(VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW
-
- runVirial(VirialExternalFieldOverlapRho.VirialExternalFieldParam) - Static method in class etomica.virial.simulations.VirialExternalFieldOverlapRho
-
- runVirial(VirialLJ.VirialLJParam) - Static method in class etomica.virial.simulations.VirialLJ
-
- runVirial(VirialLJD.VirialLJParam) - Static method in class etomica.virial.simulations.VirialLJD
-
- runVirial(VirialLJSeries.VirialLJParam) - Static method in class etomica.virial.simulations.VirialLJSeries
-
- runVirial(VirialSW.VirialSWParam) - Static method in class etomica.virial.simulations.VirialSW
-
- rv - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- rv - Variable in class etomica.potential.P2SemiclassicalMolecular.MoleculeInfoBrute
-
- Rvdw - Static variable in class etomica.potential.P2QChemInterpolated
-
- RvdwF - Variable in class etomica.potential.P2QChemInterpolated.DampingParams
-
- RvdwF - Variable in class etomica.potential.P2QChemInterpolated
-
- RvdwF - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
-
- RvdwF - Variable in class etomica.potential.P3QChem.DampingParams
-
- RYDBERG_R - Static variable in class etomica.util.Constants
-
Rydberg's constant, in Angstroms.
- rzero - Variable in class etomica.dimer.P1LepsHarmonic
-
S
- S - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- s - Static variable in class etomica.models.water.P2WaterTIP4P
-
- s - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- s - Static variable in class etomica.potential.P2O2Bartolomei
-
- s - Variable in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- s - Variable in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- s - Variable in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- s - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- s - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- s - Variable in class g3dsys.images.Line
-
- S1DHR(int, double, int) - Static method in class etomica.normalmode.NormalModes1DHR
-
Returns the analytical result for the S matrix (just a scalar in this
case) for the 1D HR system with PBC
- S2 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- S2fit(double, double, double, double, double, double, double) - Method in class etomica.models.water.P2WaterSzalewicz
-
- S3 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- sa - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- saa - Static variable in class etomica.potential.P2O2Bartolomei
-
- saaMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- saaPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- saddle - Variable in class etomica.dimer.IntegratorDimerMin
-
- saddle - Variable in class etomica.dimer.SimDimerLJadatom
-
- saddle - Variable in class etomica.dimer.SimDimerLJgb
-
- saddle - Variable in class etomica.dimer.SimDimerMEAMadatom
-
- saddle - Variable in class etomica.dimer.SimDimerMEAMGB
-
- saddleEnergy - Variable in class etomica.dimer.IntegratorDimerRT
-
- saddleFine - Variable in class etomica.dimer.SimDimerLJadatom
-
- saddleFound - Variable in class etomica.dimer.IntegratorDimerRT
-
- saddleT - Variable in class etomica.dimer.IntegratorDimerRT
-
- safeHandleOption(String[], SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.AbstractOptionHandler
-
- safeHandleOption(String[], SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.NoValueOptionHandler
-
- safeHandleOption(String[], SVGConverter) - Method in class etomica.graph.view.rasterizer.Main.SingleValueOptionHandler
-
- safetl - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- safeTruncate(float, int) - Static method in class org.jmol.util.TextFormat
-
- safetyFactor - Variable in class etomica.nbr.CriterionPositionWall
-
- safetyFactor - Variable in class etomica.nbr.CriterionSimple
-
- safetyFactor - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- sajmols - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajmolsMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajmolsPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajp1 - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajp1MRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajp1PT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajpn - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajpnMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- sajpnPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- Sam - Class in etomica.modules.sam
-
Self-assembled monolayer module.
- Sam() - Constructor for class etomica.modules.sam.Sam
-
- SamGraphic - Class in etomica.modules.sam
-
- SamGraphic(Sam) - Constructor for class etomica.modules.sam.SamGraphic
-
- SamGraphic.ActionMoveWall - Class in etomica.modules.sam
-
- SamGraphic.Applet - Class in etomica.modules.sam
-
- SamGraphic.DataPipeStressStrain - Class in etomica.modules.sam
-
- SamGraphic.ModifierWallPosition - Class in etomica.modules.sam
-
- sampleCluster - Variable in class etomica.virial.BoxCluster
-
- sampleCluster - Variable in class etomica.virial.simulations.SimulationVirial
-
- sampleClusters - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- sampleClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap
-
- sampleClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- sampleCount - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- sampleCount - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- sampleCount - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- sanityCheckBC - Variable in class etomica.data.AccumulatorAverageFixed
-
- sasurface - Static variable in class org.jmol.script.Token
-
- satisfies(Requirement) - Method in class etomica.compatibility.FeatureSet
-
- save(Parser.CommandValue) - Method in class etomica.graph.engine.Interpreter
-
- save - Static variable in class org.jmol.script.Token
-
- savedSeed - Variable in class etomica.util.random.RandomMersenneTwister
-
- savedSeedArray - Variable in class etomica.util.random.RandomMersenneTwister
-
- saveproteinstructurestate - Static variable in class org.jmol.script.Token
-
- saveValues - Variable in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- sb - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- sbet - Static variable in class etomica.potential.P2O2Bartolomei
-
- sbetMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- sbetPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- sBOType - Variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- scale - Variable in class etomica.graphics.DisplayBox
-
Factor used to scale the size of the image.
- scale - Variable in class etomica.graphics.DisplayPolytope
-
Factor used to scale the size of the image.
- scale - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
-
- scale - Variable in class etomica.virial.MCMoveClusterRingScale
-
- scale - Variable in class org.jmol.util.Quadric
-
- scale(float) - Method in class org.jmol.util.Quadric
-
- scale(float) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the scalar multiplication of itself.
- scale(float) - Method in class org.jmol.util.Tuple4f
-
Sets the value of this tuple to the scalar multiplication of itself.
- scaleAdd(float, Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the scalar multiplication of itself and
then adds tuple t1 (this = s*this + t1).
- scaleAdd(int, Tuple3i, Tuple3i) - Method in class org.jmol.util.Tuple3i
-
Sets the value of this tuple to the scalar multiplication of tuple t1 plus
tuple t2 (this = s*t1 + t2).
- scaleAdd2(float, Tuple3f, Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the scalar multiplication of tuple t1 and
then adds tuple t2 (this = s*t1 + t2).
- scaleangstromsperinch - Static variable in class org.jmol.script.Token
-
- scaleAtoms(double) - Method in class etomica.association.MCMoveVolumeAssociated
-
- scaleAtoms(double) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- scaleBox(Point3f[], float) - Static method in class org.jmol.util.BoxInfo
-
- scaleBy(double) - Method in class etomica.lattice.LatticeCubicBcc
-
Rescales the lattice by the given factor.
- scaleBy(double) - Method in class etomica.lattice.LatticeCubicDiamond
-
Rescales the lattice by the given factor.
- scaleBy(double) - Method in class etomica.lattice.LatticeCubicFcc
-
Rescales the lattice by the given factor.
- scaleBy(double) - Method in class etomica.lattice.LatticeCubicSimple
-
Rescales the lattice by the given factor.
- scaleBy(double) - Method in class etomica.lattice.LatticeHcp
-
Rescales the lattice by the given factor.
- scaleBy(double) - Method in class etomica.lattice.LatticeHcp4
-
Rescales the lattice by the given factor.
- scaleBy(double) - Method in class etomica.lattice.LatticeOrthorhombicHexagonal
-
Rescales the lattice by the given factor.
- scaledCoords0 - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- scaleFitToScreen() - Method in class g3dsys.control.G3DSys
-
- scaleMomenta() - Method in class etomica.integrator.IntegratorHard
-
Updates collision times appropriately after scaling momenta.
- scaleMomenta() - Method in class etomica.integrator.IntegratorMD
-
Crude method to enforce constant-temperature constraint, by
scaling momenta of all atoms by a constant factor so that
box adheres to setpoint temperature.
- scaleMomenta(Vector) - Method in class etomica.integrator.IntegratorMD
-
- scaleMomenta() - Method in class etomica.integrator.IntegratorRigidIterative
-
- scaleMomenta() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- scaleMomenta() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- scalePixelsPerAngstrom - Variable in class g3dsys.control.TransformManager
-
- scalePrec(BigDecimal, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Append decimal zeros to the value.
- scalePrec(BigComplex, int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Append decimal zeros to the value.
- scalePrec(BigDecimal, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Boost the precision by appending decimal zeros to the value.
- scaleSetSize(int, int) - Method in class etomica.graphics.DisplayBoxCanvas1D
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSetSize(int, int) - Method in class etomica.graphics.DisplayBoxCanvas2D
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSetSize(int, int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSetSize(int, int) - Method in class etomica.graphics.DisplayPolytopeCanvas2D
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSetSize(int, int) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSetSize(int, int) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
Sets the size of the display to a new value and scales the image so that
the box fits in the canvas in the same proportion as before.
- scaleSize(double) - Method in class etomica.lattice.crystal.Primitive
-
Scales (multiplies) the size of each primitive vector by the given value.
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveBcc
-
Multiplies the size of the current vectors by the given value.
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveCubic
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveFcc
-
Multiplies the size of the current vectors by the given value.
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveGeneral
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- scaleSize(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- scaleSize(double) - Method in class etomica.models.hexane.PrimitiveHexane
-
- scaleSlider - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- scaleVector - Variable in class etomica.action.BoxInflate
-
- scaleVector - Variable in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- scaleVector - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- scaling - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- scaling - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- scBeads - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- scf - Variable in class etomica.potential.P2QChemInterpolated
-
- scf - Variable in class etomica.potential.P3AdditiveQChem.DampingParams
-
- scfAtoms - Variable in class etomica.virial.ClusterSumPolarizable
-
- scfAtoms - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- scfAtoms - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- scfAtoms - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- ScientificFormat - Class in etomica.util
-
a formatter that uses a format suitable for numeric values in a
scientific context.
- ScientificFormat() - Constructor for class etomica.util.ScientificFormat
-
Create a ScientificFormat using the default pattern and symbols
for the default locale.
- ScientificFormat(Locale) - Constructor for class etomica.util.ScientificFormat
-
Create a ScientificFormat using the default pattern for the
given locale.
- ScientificFormat(String) - Constructor for class etomica.util.ScientificFormat
-
Creates a ScientificFormat using a given pattern
- ScientificFormat(Locale, String) - Constructor for class etomica.util.ScientificFormat
-
Creates a ScientificFormat using a given pattern for the specified
locale
- scoreGreaterThan(int[]) - Method in class etomica.virial.cluster.ClusterDiagram
-
Determines if the cluster's current configuration has a score greater
than the given score.
- screenDiameter - Variable in class org.jmol.util.Point3fi
-
- screened - Variable in class etomica.virial.ClusterWheatleyHS
-
- screened - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- screenSpace(Point3f, Point3i) - Method in class g3dsys.control.G3DSys
-
Converts molspace point p (in Angstroms) to a point on the display
in pixels.
- screenx - Static variable in class org.jmol.script.Token
-
- screenX - Variable in class org.jmol.util.Point3fi
-
- screenxyz - Static variable in class org.jmol.script.Token
-
- screeny - Static variable in class org.jmol.script.Token
-
- screenY - Variable in class org.jmol.util.Point3fi
-
- screenz - Static variable in class org.jmol.script.Token
-
- screenZ - Variable in class org.jmol.util.Point3fi
-
- SCRIPT_EDITOR_IGNORE - Static variable in class org.jmol.viewer.JmolConstants
-
- scriptCommand - Static variable in class org.jmol.script.Token
-
- scriptqueue - Static variable in class org.jmol.script.Token
-
- scriptreportinglevel - Static variable in class org.jmol.script.Token
-
- ScriptVariable - Class in org.jmol.script
-
- ScriptVariable(int) - Constructor for class org.jmol.script.ScriptVariable
-
- ScriptVariable.Sort - Class in org.jmol.script
-
- ScriptVariableInt - Class in org.jmol.script
-
- ScriptVariableInt(int) - Constructor for class org.jmol.script.ScriptVariableInt
-
- SearchState - Interface in etomica.graph.isomorphism
-
- secDerXr - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- secDerXr - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- Second - Class in etomica.units
-
- secondaryBox - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- secondaryBox - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- secondaryCoordDef - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- secondaryCoordDef - Variable in class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- secondaryDirection - Variable in class etomica.config.ConfigurationOrientedFile
-
- secondaryDirection - Variable in class etomica.space3d.OrientationFull3D
-
- secondAxis - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- secondAxis - Variable in class etomica.association.BiasVolumeAceticAcid
-
- secondBox - Variable in class etomica.integrator.mcmove.MCMoveVolumeExchange
-
- secondder - Variable in class etomica.meam.PotentialCuLREP
-
- secondder(IAtomList) - Method in class etomica.meam.PotentialCuLREP
-
- secondder - Variable in class etomica.meam.PotentialEAM
-
- secondder(IAtomList) - Method in class etomica.meam.PotentialEAM
-
- secondder - Variable in class etomica.meam.PotentialEAM_LS
-
- secondder - Variable in class etomica.meam.PotentialEFS
-
- secondder(IAtomList) - Method in class etomica.meam.PotentialEFS
-
- secondDerivative(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- secondDerivative - Variable in class etomica.models.water.P2Water4PSoft
-
- secondDerivative(IMoleculeList) - Method in class etomica.models.water.P2Water4PSoft
-
- secondDerivative - Variable in class etomica.potential.EwaldSummation
-
- secondDerivative(IAtom, IAtom) - Method in class etomica.potential.EwaldSummation
-
- secondDerivative(IMoleculeList) - Method in interface etomica.potential.IPotentialMolecularSecondDerivative
-
- secondDerivative - Variable in class etomica.potential.P2HSDipole
-
- secondDerivative(IMoleculeList) - Method in class etomica.potential.P2HSDipole
-
- secondDerivative - Variable in class etomica.potential.P2LJDipole
-
- secondDerivative(IMoleculeList) - Method in class etomica.potential.P2LJDipole
-
- secondDerivative - Variable in class etomica.potential.P2ReactionFieldDipole
-
- secondDerivative(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole
-
- secondDerivativeSum - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- secondDerivativeSum - Variable in class etomica.potential.PotentialCalculationPhiSum
-
- secondDerivativeXr(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- secondDerivativeXrRotRot(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- securityOff - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Controls whether scripts should be run securely or not
- seed - Variable in class etomica.virial.simulations.VirialH2OGCPMD.VirialParam
-
- seed - Variable in class etomica.virial.simulations.VirialRowleyAlcohol.VirialParam
-
- SEED_COUNT - Static variable in class org.jmol.util.MeshSurface
-
- seeds - Variable in class etomica.simulation.Simulation
-
- seen(byte) - Method in class etomica.graph.traversal.AbstractTraversal
-
- seenAll() - Method in class etomica.graph.traversal.AbstractTraversal
-
- seenArrays - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
-
- seenParams - Variable in class etomica.modules.multiharmonic.overlap.DataOverlapCaching
-
- segment - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- segmentList - Variable in class etomica.graph.property.FFTDecomposition
-
- selectallmodels - Static variable in class org.jmol.script.Token
-
- selected - Static variable in class org.jmol.script.Token
-
- selectedAtoms - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- selectedAtoms - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- selectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- selectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- selectedAtoms - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- selectedfloat - Static variable in class org.jmol.script.Token
-
- selectedMolecules - Variable in class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- selectedMolecules - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- selectedMolecules - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- selecthetero - Static variable in class org.jmol.script.Token
-
- selecthydrogen - Static variable in class org.jmol.script.Token
-
- selectionForKey(char, ComboBoxModel) - Method in class etomica.graphics.DimensionedDoubleEditor
-
Implementation of KeySelectionManager interface that uses key press to
select a unit prefix (instead of selecting a combo box item).
- selectionhalos - Static variable in class org.jmol.script.Token
-
- selectItemTok(Token) - Static method in class org.jmol.script.ScriptVariable
-
- selectItemTok(Token, int) - Static method in class org.jmol.script.ScriptVariable
-
- selectItemVar(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- selectItemVar2(ScriptVariable, int) - Static method in class org.jmol.script.ScriptVariable
-
- selectMolecules() - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- selectMolecules() - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- selectMolecules() - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- selectMove() - Method in class etomica.integrator.mcmove.MCMoveManager
-
Selects a MCMove instance from among those added to the integrator, with
probability in proportion to the frequency value assigned to the move.
- selfELJ - Static variable in class etomica.models.clathrates.MinimizationTIP4P
-
- semiClassical - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- semiClassical - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- semiClassical - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- semiClassical - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- semiClassical - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- sep - Variable in class etomica.models.water.P2WaterSzalewicz
-
- separationProbability(int, double) - Static method in class etomica.virial.MCMoveClusterAtomHSRing
-
Normalized probability for the separation of the centers of two spheres located at the
end of a chain of (n+1) overlapping spheres.
- seq - Variable in class etomica.virial.MCMoveClusterAtomHSChain
-
- seq - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- seq - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
-
- sequence - Static variable in class org.jmol.script.Token
-
- serial - Variable in class etomica.modules.droplet.EllipseDisplayAction
-
- serialize(Vector, JsonGenerator, SerializerProvider) - Method in class etomica.meta.serializers.VectorSerializer
-
- serialize(IData, JsonGenerator, SerializerProvider) - Method in class etomica.server.serializers.DataSerializer
-
- serialize(Property, JsonGenerator, SerializerProvider) - Method in class etomica.server.serializers.PropertySerializer
-
- serialize(Wrapper<?>, JsonGenerator, SerializerProvider) - Method in class etomica.server.serializers.WrapperSerializer
-
- serialVersionUID - Static variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- serialVersionUID - Static variable in class etomica.models.rowley.DimerApproach
-
- set(int, IAtom) - Method in class etomica.atom.AtomArrayList
-
- set(Parser.CommandPropertyValue) - Method in class etomica.graph.engine.Interpreter
-
- set(int, IMolecule) - Method in class etomica.molecule.MoleculeArrayList
-
- set(int, Rational) - Method in class etomica.veos.bigdecimal.Bernoulli
-
Set a coefficient in the internal table.
- set(int, BigInteger) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Set a polynomial coefficient.
- set(int, int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Set a polynomial coefficient.
- set(int) - Method in class etomica.veos.bigdecimal.Euler
-
Compute a coefficient in the internal table.
- set(ScriptVariable, boolean) - Method in class org.jmol.script.ScriptVariable
-
creates a NEW version of the variable
- set(int) - Method in class org.jmol.util.BitSet
-
Sets the bit at the specified index to true.
- set(Quaternion) - Method in class org.jmol.util.Quaternion
-
- set(float, float, float) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the specified xyz coordinates.
- set(int, int, int) - Method in class org.jmol.util.Tuple3i
-
Sets the value of this tuple to to the specified x, y, and z coordinates.
- set(float, float, float, float) - Method in class org.jmol.util.Tuple4f
-
Sets the value of this tuple to the specified xyzw coordinates.
- set2(Point3f, Point3i) - Static method in class org.jmol.util.Point3fi
-
- set4(float, float, float, float) - Method in class org.jmol.util.AxisAngle4f
-
Sets the value of this axis angle to the specified x,y,z,angle.
- set_sites(Vector[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- set_sites_itypea - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- set_sites_sa - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- set_sites_sitea - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- setA(double) - Method in class etomica.models.hexane.PrimitiveHexane
-
Sets A and scales B and C to maintain relative size
- setA(double) - Method in class etomica.modules.rheology.IntegratorPolymer
-
- setA(double) - Method in class etomica.potential.P2Exp6
-
- setA(int, double) - Method in class etomica.potential.P2HeSimplified
-
Sets the ith parameter value
u = A0 * exp(-A1*r) - A2/r^6 - A3/r^X
where X = 10 if useC10 is true, X=8 otherwise
- setA(double) - Method in class etomica.potential.P2ModifiedMorse
-
- setA(double) - Method in class etomica.potential.P2Morse
-
- setA() - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- setA() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setA(float[]) - Method in class org.jmol.util.Matrix3f
-
Sets the values in this Matrix3f equal to the row-major array parameter
(ie, the first four elements of the array will be copied into the first row
of this matrix, etc.).
- setA(float[]) - Method in class org.jmol.util.Matrix4f
-
Sets the values in this Matrix4f equal to the row-major array parameter
(ie, the first four elements of the array will be copied into the first row
of this matrix, etc.).
- setA(float[]) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple from the 3 values specified in the array.
- setAA(AxisAngle4f) - Method in class org.jmol.util.AxisAngle4f
-
Sets the value of this axis angle to the value of axis angle t1.
- setAA(AxisAngle4f) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to the matrix conversion of the single
precision axis and angle argument.
- setAA(AxisAngle4f) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to the matrix conversion of the single
precision axis and angle argument.
- setAA(AxisAngle4f) - Method in class org.jmol.util.Quaternion
-
- setABC(int) - Method in class org.jmol.util.MeshSurface
-
- setAcceptanceTarget(double) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
Sets the desired rate of acceptance (as a fraction between 0 and 1
inclusive) of trials of this move.
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- setAccumulator(AccumulatorAverage) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
Specifies the accumulator that generates the displayed values.
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- setAccumulator(AccumulatorAverageCollapsingLog) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
-
- setAccumulator(AccumulatorAverageCollapsingLog) - Method in class etomica.modules.multiharmonic.DataProcessorVar
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlap
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapLJ
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphere
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.normalmode.SimOverlapSSnxy
-
- setAccumulator(IDataSink) - Method in class etomica.virial.simulations.SimulationVirial
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- setAccumulator(AccumulatorVirialOverlapSingleAverage, int) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImage
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setAccumulatorBlockSize(int) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setAccumulatorBlockSize(long) - Method in class etomica.virial.simulations.SimulationVirial
-
- setAccumulatorBlockSize(int) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- setAccumulatorBlockSize(long) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- setAccumulatorBlockSize(long) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setAccumulators(AccumulatorAverageCollapsingLog[]) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- setAccumulatorUpdateInterval(int) - Method in class etomica.data.DataTableAverages
-
Sets the interval for updates to the accumulators feeding this table.
- setAction(IAction) - Method in class etomica.graphics.DeviceButton
-
Defines the action to be performed when the button is pressed.
- setAction(IntegratorAnalytic.AtomTimeAction) - Method in class etomica.integrator.IntegratorAnalytic
-
- setAction(IAction) - Method in class etomica.zeolite.DeviceButtonSingle
-
Defines the action to be performed when the button is pressed.
- setActions(IAction[]) - Method in class etomica.action.activity.ActivityGroupParallel
-
- setActive(boolean) - Method in class etomica.data.DataAccumulator
-
- setActive(int, boolean, boolean) - Method in class etomica.potential.P1HardBoundary
-
- setActiveLevel(int, boolean) - Static method in class org.jmol.util.Logger
-
Changes the activation state for a logging level.
- setActivityIntegrate(ActivityIntegrate) - Method in class etomica.dimer.IntegratorDimerMin
-
- setActivityIntegrate(ActivityIntegrate) - Method in class etomica.dimer.IntegratorDimerRT
-
- setAddAnotherSpecies(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddPotential(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddPotential(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setAddSameSpecies(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddSpecies(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddSpecies1(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddSpecies2(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAddSpecies3(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAdiabatic() - Method in class etomica.graphics.DeviceThermoSlider
-
Set the Adiabatic button to its selected state.
- setAdiabatic() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the Adiabatic button to its selected state.
- setAdjustInterval(long) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
Sets the interval between steps size adjustments.
- setAdjustInterval(long) - Method in class etomica.overlap.IntegratorOverlap
-
Sets how frequently the appropriate reference vs.
- setAdjustStepFraction(boolean) - Method in class etomica.overlap.IntegratorOverlap
-
Sets whether to adjust the number of relative number of steps for each
sub-integrator.
- setAdjustStepFreq(boolean) - Method in class etomica.virial.overlap.IntegratorOverlap
-
Sets whether to adjust the number of relative number of steps for each
sub-integrator.
- setAdjustStepSize(double) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
Sets the step adjustment size.
- setAelement(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- setAffectedWV(int) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setAffectedWV(int) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setAffectedWV(int) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setAgent(IAtom, E) - Method in class etomica.atom.AtomLeafAgentManager
-
Sets the agent associated with the given atom to be the given agent.
- setAgent(AtomType, E) - Method in class etomica.atom.AtomTypeAgentManager
-
Sets the agent associated with the given atom type to be the given agent.
- setAgent(Box, E) - Method in class etomica.box.BoxAgentManager
-
Associates an Agent with a Box.
- setAgent(IMolecule, E) - Method in class etomica.molecule.MoleculeAgentManager
-
Sets the agent associated with the given atom to be the given agent.
- setAgent(ISpecies, E) - Method in class etomica.species.SpeciesAgentManager
-
Sets the agent associated with the given atom type to be the given
agent.
- setAgentManager(AtomLeafAgentManager<IntegratorHard.Agent>) - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp
-
- setAgentManager(AtomLeafAgentManager) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
- setAgentManager(AtomLeafAgentManager<AtomPotentialList>) - Method in class etomica.nbr.list.NeighborListManager.AtomPotential1ListSource
-
- setAgentManager(AtomLeafAgentManager<? extends Integrator.Forcible>) - Method in class etomica.potential.PotentialCalculationForceSum
-
- setAgentManager(AtomLeafAgentManager<?>) - Method in class etomica.potential.PotentialCalculationTorqueSum
-
- setAgentManager(AtomLeafAgentManager<? extends Integrator.Forcible>) - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- setAggressiveAdjustStepFraction(boolean) - Method in class etomica.overlap.IntegratorOverlap
-
Sets whether to use "aggressive" adjustment.
- setAlertMessage(String) - Method in class etomica.virial.GUI.models.ModelAlertMsgDialog
-
- setAlertMsgBoxController(ControllerAlertMsgBox) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- setAlertMsgBoxSpeciesRemoval(ViewAlertMsgBoxSpeciesRemoval) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setAlign(int, int) - Method in class etomica.graphics.DisplayBox
-
- setAlign(int, int) - Method in class etomica.graphics.DisplayPolytope
-
- setAlkaneIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setAlkaneIndex(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setAlkaneLength(int, int) - Method in class etomica.virial.GUI.models.ModelAlkaneLengthSelection
-
- setAlkaneLengthSelectionDM(ModelAlkaneLengthSelection) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- setAlkaneLengthSelectionView(ViewAlkaneLengthSelection, int) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- setAll(int) - Static method in class org.jmol.util.BitSetUtil
-
- setAllEVal() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the "All eigenvalues" button to its selected state.
- setAllowedScriptTypes(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the set of allowed script types (i.e., the set of possible
values for the type attribute in the <script> element),
as a comma separated list of allowed values.
- setAllowEqualElements(boolean) - Method in class etomica.lattice.IndexIteratorTriangular
-
Sets flag indicating whether iterates may have elements that are equal to one another.
- setAllPermutations(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to generate all permutations.
- setAllPermutations(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setAllPermutations(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setAllUnits(Unit) - Method in class etomica.graphics.DisplayTable
-
Sets the units of all columns to the given unit.
- setAllWV() - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the "All Wave Vectors" button to its selected state.
- setAlpha(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- setAlpha(double[]) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setAlpha(double[]) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setAlpha(double[], double[]) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
sets the range of parameter values used for Bennets method.
- setAlpha(double) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- setAlpha(double) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- setAlpha(double) - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- setAlpha(double[]) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setAlpha(double[]) - Method in class etomica.normalmode.MeterTargetTP
-
- setAlpha(double, double) - Method in class etomica.normalmode.SimOverlapModule
-
- setAlpha(double) - Method in class etomica.potential.EwaldSummation
-
- setAlpha(double) - Method in class etomica.potential.P2Dreiding
-
- setAlpha(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setAlpha() - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- setAlpha() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setAlphaCenter(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- setAlphaEin(double) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
Sets the Einstein spring constant
u = alpha * r^2
- setAlphaEin(double) - Method in class etomica.normalmode.MCMoveHarmonicEin
-
Sets the Einstein spring constant
- setAlphaFac(double) - Method in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- setAlphaRange(double, double) - Method in class etomica.overlap.MeterOverlap
-
sets the range of parameter values used for Bennets method.
- setAlphaSpan(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setAlphaSpan(double) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setAlphaSpan(double) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setAlphaSpan(double) - Method in class etomica.normalmode.MeterTargetTP
-
- setAlternateStylesheet(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the alternateStyleSheet value.
- setAlterSimEnv(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setAlterSimEnv(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setAmbientPercent(int) - Static method in class org.jmol.util.GData
-
fractional distance from black for ambient color
- setAmplitude(double) - Method in class etomica.potential.P2Fene
-
- setAndIncrement(Rgb16, Rgb16) - Method in class org.jmol.util.Rgb16
-
- setAngle(int, double) - Method in class etomica.config.ConformationChainLinear
-
- setAngle(int, double) - Method in class etomica.config.ConformationLinear
-
- setAngle(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setAngle(double) - Method in class etomica.potential.P3BondAngle
-
Sets the nominal bond angle (in radians)
- setAngle(double) - Method in class etomica.potential.P3BondAngleDreiding
-
Sets the nominal bond angle (in radians)
- setAngle(double) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
Sets the nominal bond angle (in radians)
- setAngleAlpha(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setAngleBeta(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- setAngleBeta(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setAngleGamma(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setAngles(double, double, double) - Method in class etomica.action.AtomActionRotateBy
-
- setAngles(double[]) - Method in class etomica.lattice.crystal.Primitive
-
Sets the angles between the primitive vector to the corresponding
values in the given array.
- setAngles(double[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- setAnharmonicConstant(double) - Method in class etomica.potential.P2Anharmonic
-
- setAppending(boolean) - Method in class etomica.data.DataLogger
-
Overwrite or attach the data to the file.
- setApplyToMolecules(boolean) - Method in class etomica.action.BoxImposePbc
-
Sets a flag indicating whether periodic boundaries are applied to the
molecules (true), or to the atoms (false).
- setApproximation(int) - Method in class etomica.virial.cluster.ClusterOperations
-
- setArea(Rectangle2D) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the area as a Rectangle.
- setArray(double[][]) - Method in class etomica.eigenstuff.MyEigenvalueDecomposition
-
- setArrayList(AtomArrayList) - Method in class etomica.atom.AtomToAtomSetFixed
-
- setArrayList(MoleculeArrayList) - Method in class etomica.molecule.MoleculeToMoleculeSetFixed
-
- setArrayListPotentialCollection(ArrayList<ICollectionPotential>) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- setArrayShape(int[]) - Method in class etomica.data.types.DataDoubleArray.DataInfoDoubleArrayFactory
-
Sets the array shape.
- setArrayShape(int[]) - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
-
Sets the array shape.
- setAsCube(double) - Method in class etomica.space.BoundaryDeformablePeriodic
-
Sets the shape of the boundary to a cube with edges equal to the given value.
- setAspect(float) - Method in class g3dsys.images.Ellipse
-
- setAsRectangular(Vector) - Method in class etomica.space.BoundaryDeformablePeriodic
-
Sets the shape of the boundary as a rectangular parallelepiped (or
parallelogram) with edge lengths given by the elements of the given
vector.
- setAssociationManager(AssociationManager) - Method in class etomica.association.AtomSourceRandomDimer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.AtomSourceRandomMonomer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.AtomSourceRandomSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomDimer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomMonomer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomNoSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveAtomSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveBiasUB
-
- setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveBiasUBMolecule
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveDimer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveDimerRotate
-
- setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveMoleculeMonomer
-
- setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveMoleculeRotateAssociated
-
- setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveMoleculeSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveRotateAssociated
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveRotateNoSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveSmer
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveSmerRotate
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MCMoveVolumeAssociated
-
- setAssociationManager(AssociationManagerMolecule, IAssociationHelperMolecule) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- setAssociationManager(AssociationManager) - Method in class etomica.association.MeterDimerMoleFraction
-
- setAssociationManager(AssociationManagerMolecule) - Method in class etomica.association.MoleculeSourceRandomDimer
-
- setAssociationManager(AssociationManagerMolecule) - Method in class etomica.association.MoleculeSourceRandomMonomer
-
- setAsText(String) - Method in class etomica.graphics.DimensionedDoubleEditor
-
Sets the value, interpreted as being in the editor's units, from a text string.
- setAtom(IAtom) - Method in class etomica.atom.iterator.AtomIteratorArrayList
-
Sets the first atom for iteration.
- setAtom(IAtom) - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
Sets the first atom for iteration.
- setAtom(IAtom) - Method in interface etomica.atom.iterator.AtomIteratorAtomDependent
-
- setAtom(IAtom) - Method in class etomica.atom.iterator.AtomIteratorSinglet
-
Defines atom returned by iterator and leaves iterator unset.
- setAtom(IAtom) - Method in class etomica.graphics.ColorSchemeNeighbor
-
- setAtom(IAtom) - Method in class etomica.graphics.ColorSchemeNeighborCell
-
- setAtom(IAtom) - Method in class etomica.integrator.IntegratorHard.CollisionHandlerUp
-
sets the atom whose collision time is to be calculated
- setAtom(IAtom) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- setAtom(IAtom) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- setAtom(IAtom) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- setAtom(IAtom) - Method in class etomica.nbr.site.AtomSite
-
- setAtomAgentManager(Box, AtomLeafAgentManager<? extends Vector>) - Method in class etomica.potential.P1HarmonicSite
-
- setAtomFilter(AtomFilter) - Method in class etomica.graphics.DisplayBox
-
Mutator method for the atom filter that determines which atoms
are displayed.
- setAtomInfo(AtomType, P2SemiclassicalAtomic.AtomInfo) - Method in class etomica.potential.P2SemiclassicalAtomic
-
- setAtomNumber(int) - Method in class etomica.modules.materialfracture.MeterElongation
-
- setAtomNumber(int) - Method in class etomica.modules.materialfracture.MeterStrain
-
- setAtomPositionDefinition(IMoleculePositionDefinition) - Method in class etomica.action.MoleculeActionTranslateTo
-
- setAtomPositionDefinition(IMoleculePositionDefinition) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
- setAtomPositionDefinition(IMoleculePositionDefinition) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
- setAtoms(IAtomList) - Method in class etomica.atom.AtomListWrapper
-
Copies the atoms in the given atom set to the wrapped array of atoms.
- setAtoms(IAtom[]) - Method in class etomica.atom.AtomsetArray
-
Copies the atoms in the given array to the wrapped, final array of atoms.
- setAtoms(IAtomList) - Method in class etomica.atom.AtomsetArray
-
Copies the atoms in the given atom set to the wrapped array of atoms.
- setAtoms(IAtom, IAtom) - Method in class etomica.data.DataSourceAtomDistance
-
- setAtoms(IAtomList) - Method in class etomica.data.meter.MeterStructureFactor
-
- setAtoms(IMoleculeList) - Method in class etomica.molecule.MoleculeListWrapper
-
Copies the atoms in the given atom set to the wrapped array of atoms.
- setAtoms(IMolecule[]) - Method in class etomica.molecule.MoleculesetArray
-
Copies the atoms in the given array to the wrapped, final array of atoms.
- setAtoms(IMoleculeList) - Method in class etomica.molecule.MoleculesetArray
-
Copies the atoms in the given atom set to the wrapped array of atoms.
- setAtomSource(AtomSource) - Method in class etomica.association.MCMoveDimer
-
- setAtomSource(AtomSource) - Method in class etomica.association.MCMoveDimerRotate
-
- setAtomSource(AtomSource) - Method in class etomica.association.MCMoveSmer
-
- setAtomSource(AtomSource) - Method in class etomica.association.MCMoveSmerRotate
-
- setAtomSource(AtomSource) - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- setAtomSource(AtomSource) - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- setAtomSource(AtomSource) - Method in class etomica.integrator.mcmove.MCMoveAtom
-
- setAtomSource(AtomSource) - Method in class etomica.integrator.mcmove.MCMoveDimer
-
- setAtomSource(AtomSource) - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- setAtomSource(MoleculeSource) - Method in class etomica.models.hexane.MCMoveReptate
-
- setAtomSource(AtomSource) - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- setAtomSource(AtomSource) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- setAtomSource(AtomSource) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setAtomSource(AtomSource) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setAtomSource(AtomSource) - Method in class etomica.virial.MCMoveClusterAtomQ
-
- setAtomType(AtomType) - Method in class etomica.data.meter.MeterRDF
-
- setAtomType(AtomType) - Method in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
-
- setAtomType(AtomType) - Method in class etomica.mappedRdf.MeterMappedRdf
-
- setAtomTypes(AtomType, AtomType) - Method in class etomica.data.meter.MeterRDF
-
- setAtomTypes(AtomType, AtomType) - Method in class etomica.mappedRdf.MeterMappedRdf
-
- setAutoScale(boolean) - Method in class etomica.graphics.DevicePlotPoints
-
- setAvgDef(boolean) - Method in class etomica.normalmode.DataSourceFE
-
- setAxial(int, double) - Method in interface etomica.space.RotationTensor
-
- setAxial(int, double) - Method in class etomica.space1d.RotationTensor1D
-
- setAxial(int, double) - Method in class etomica.space2d.RotationTensor2D
-
- setAxial(int, double) - Method in class etomica.space3d.RotationTensor3D
-
Sets tensor for rotation about the indicated axis (0=x,1=y,2=z) by
the given angle.
- setAxisSymmetric(boolean) - Method in class etomica.species.SpeciesSpheresRotating
-
- setB(double) - Method in class etomica.modules.rheology.IntegratorPolymer
-
- setB(double) - Method in class etomica.modules.sam.P1Sinusoidal
-
- setB(double) - Method in class etomica.potential.P2Exp6
-
- setBackgroundArgb(int) - Method in class org.jmol.util.GData
-
sets background color to the specified argb value
- setBackgroundColor(Color) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the backgroundColor value.
- setBackgroundColor(Color) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Sets the background color of the display box canvas.
- setBackgroundColor(Color) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Sets the background color of the display box canvas.
- setBackgroundImage(Object) - Method in class org.jmol.util.GData
-
- setBackgroundTransparent(boolean) - Method in class org.jmol.g3d.Graphics3D
-
- setBackgroundTransparent(boolean) - Method in class org.jmol.util.GData
-
- setBarrier(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- setBarrier(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- setBarrier(double) - Method in class etomica.modules.reactionequilibrium.P2SquareWellBonded
-
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
Specifies the basis, which identifies the molecules subject to
iteration.
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ANIntergroupExchange
-
Specifies the basis, which identifies the molecules subject to
iteration.
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ANIntragroupExchange
-
Specifies the basis, which identifies the molecules subject to
iteration.
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIndexList
-
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIntergroup
-
Specifies the basis, which identifies the atoms subject to iteration.
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIntergroupExchange
-
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.ApiIntragroup
-
Specifies the parent atom of the iterates.
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.AtomIteratorBasis
-
Sets the basis for iteration, such that the childList atoms of the given
atom will be subject to iteration (within any specifications given by a
prior or subsequent call to setTarget).
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart
-
Sets the basis for iteration, such that the childList atoms of the given
atom will be subject to iteration (within any specifications given by a
prior or subsequent call to setTarget).
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
- setBasis(IMoleculeList) - Method in interface etomica.atom.iterator.AtomsetIteratorBasisDependent
-
Identifies the atoms that form the basis for iteration, such that
the childList atoms of those given will form the iterates.
- setBasis(IMoleculeList) - Method in class etomica.atom.iterator.TripletInnerSequential
-
- setBasis(IMoleculeList) - Method in interface etomica.molecule.iterator.MoleculesetIteratorBasisDependent
-
- setBasis(IMoleculeList) - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- setBasisMolecules(Basis) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setBasisMonoclinic() - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- setBasisOrthorhombic() - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- setBasisSurface(Basis) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setBbcage(float) - Method in class org.jmol.util.BoxInfo
-
- setBennetParam(double, double) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
sets the range of parameter values used for Bennets method.
- setBennetParam(double, double) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
sets the range of parameter values used for Bennets method.
- setBennetParam(double, double) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
sets the range of parameter values used for Bennets method.
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImage
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImage
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1D
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setBennettParameter(double, double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setBennettParameter(double) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setBeta(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- setBeta(double) - Method in class etomica.potential.P4TorsionDreiding
-
- setBeta3() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setBeta4211() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setBeta4220() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setBetaPhase(boolean) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setBetaPositionAndOrientation(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setBGColor(Color) - Method in class g3dsys.control.G3DSys
-
Change the background color of the G3D display
- setBiasCubeDimensions(Vector) - Method in class etomica.association.BiasVolumeCube
-
- setBiasCubeDimensions(double) - Method in class etomica.association.BiasVolumeCube
-
- setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeAceticAcid
-
- setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeSphere
-
- setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeSphereOriented
-
- setBiasSphereInnerRadius(double) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
- setBiasSphereRadius(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeAceticAcid
-
- setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeSphere
-
- setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeSphereOriented
-
- setBiasSphereRadius(double) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
- setBiasVolume(BiasVolume2SiteAceticAcid) - Method in class etomica.models.OPLS.P2AceticAcidTwoSite
-
- setBiasVolume(BiasVolume2SiteAceticAcid) - Method in class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
-
- setBinSize(double) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- setBit(int) - Method in interface etomica.graph.model.Bitmap
-
- setBit(int) - Method in class etomica.graph.model.impl.BitmapOfLong
-
The highest order bit is at bit 0 of bitmap, and the lowest order bit is at bit
bitSize() - 1 of bitmap.
- setBit(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
The highest order bit is at bit 0 of bitmap[0], and the lowest order bit is at bit
bitSize() - 1 of bitmap[size()-1].
- setBits(boolean) - Method in interface etomica.graph.model.Bitmap
-
- setBits(boolean) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- setBits(boolean) - Method in class etomica.graph.model.impl.BitmapOfLong
-
TIME = O(1).
- setBits(boolean) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- setBits(int, int) - Method in class org.jmol.util.BitSet
-
Sets the bits from the specified fromIndex (inclusive) to the
specified toIndex (exclusive) to true.
- setBitSize(int) - Method in class etomica.graph.model.impl.BitmapOfLong
-
- setBitSize(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- setBitTo(int, boolean) - Method in class org.jmol.util.BitSet
-
Sets the bit at the specified index to the specified value.
- setBlockDataSink(IDataSink) - Method in class etomica.data.AccumulatorAverageFixed
-
Allows individual block data to be passed to a data sink.
- setBlockSize(long) - Method in class etomica.data.AccumulatorAverage
-
Sets the size of the block used to group data for error analysis.
- setBlockSize(long) - Method in class etomica.data.AccumulatorAverageCollapsing
-
Sets the size of the block used to group data for error analysis.
- setBondConstraints(ISpecies, int[][], double[]) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- setBondDelta(double) - Method in class etomica.potential.P2HardBond
-
Sets the bond extension factor (max = length * (1+delta))
- setBondDelta(double) - Method in class etomica.potential.P2PenetrableBond
-
Sets the bond extension factor (max = length * (1+delta))
- setBonded(boolean) - Method in class etomica.nbr.CriterionBondedSimple
-
- setBonded(boolean, IAtom, IAtom, double) - Method in class etomica.potential.P2HardBondedList
-
Adds/removes the pair of atoms to/from each other's bonded list.
- setBondedSurfaceAtoms(IMolecule, IAtomList) - Method in class etomica.modules.sam.CriterionTether3
-
- setBondFac(double) - Method in class etomica.modules.colloid.P2HardSphereMC
-
- setBondFac(double) - Method in class etomica.modules.colloid.P2SquareWellMonomer
-
- setBondingPotential(Potential2) - Method in class etomica.chem.models.ModelChain
-
Set the bonding potential for adjacent atoms in the chain molecule.
- setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setBondL(double) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setBondL(double) - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- setBondL(double) - Method in class etomica.virial.SpeciesFactorySpheres2
-
- setBondLength(double) - Method in class etomica.atom.AtomHydrogen
-
- setBondLength(double) - Method in class etomica.config.ConformationChainLinear
-
- setBondLength(double) - Method in class etomica.config.ConformationLinear
-
- setBondLength(double) - Method in class etomica.models.hexane.CBMCGrowSolidHexane
-
- setBondLength(double) - Method in class etomica.potential.P2Dreiding
-
- setBondLength(double) - Method in class etomica.potential.P2HardBond
-
Setter method for the bond length
- setBondLength(double) - Method in class etomica.potential.P2PenetrableBond
-
Setter method for the bond length
- setBondLength(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setBondLength(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setBondLength(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setBondLength(double) - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- setBondLength(double) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- setBondLength(double) - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- setBondLengths(double[]) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- setBonds(int[][]) - Method in class etomica.virial.cluster.ClusterCollapsedTreeNode
-
- setBonds(int[]) - Method in class etomica.virial.cluster.ClusterTreeNode
-
- setBondTheta(double) - Method in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- setBondTheta(double) - Method in class etomica.virial.SpeciesFactorySpheres2
-
- setBondType(int) - Method in class etomica.models.water.P2HardAssociationGCPMReference
-
- setBondType(int) - Method in class etomica.models.water.PNWaterGCPMThreeSite
-
- setBondType(int) - Method in class g3dsys.images.Bond
-
- setBoolean(boolean) - Method in class etomica.integrator.IntegratorGear4NPH.EnsembleToggler
-
- setBoolean(boolean) - Method in interface etomica.modifier.ModifierBoolean
-
Sets the modified value to the given boolean.
- setBoolean(boolean) - Method in class etomica.modules.joulethomson.IntegratorJT.EnsembleToggler
-
- setBorderAlignment(int) - Method in class etomica.graphics.DeviceSlider
-
- setBorderAlignment(int) - Method in class etomica.graphics.DeviceSpinner
-
- setBorderBackground(Color) - Method in class etomica.graphics.DeviceBox
-
- setBoundaries(int, double[], int[]) - Method in class etomica.modules.rosmosis.MeterFlux
-
- setBoundary(Boundary) - Method in class etomica.box.Box
-
Sets the box's boundary to the given Boundary.
- setBoundaryFrameColor(Color) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Sets the color of the box boundary.
- setBoundaryFrameColor(Color) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Sets the color of the box boundary.
- setBoundaryPadding(double) - Method in class etomica.config.ConfigurationLattice
-
- setBoundaryVectors(double[]) - Method in class g3dsys.control.G3DSys
-
Sets the boundary vectors to be used for calculating image shells
- setBoundaryVectors(double[]) - Method in class g3dsys.images.ImageShell
-
- setBoundaryVectorsIterator(IndexIterator) - Method in class g3dsys.control.G3DSys
-
Sets the index iterator to use for calculating image shells
- setBoundaryVectorsIterator(IndexIterator) - Method in class g3dsys.images.ImageShell
-
- setBoundaryWall(boolean) - Method in class etomica.nbr.CriterionPositionWall
-
Sets whether the walls are at the box boundaries or not.
- setBoundBox(Point3f, Point3f, boolean, float) - Method in class org.jmol.util.BoxInfo
-
- setBoundingBox(Vector, Vector) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Sets the display bounding box.
- setBoundingBox(float, float, float, float, float, float) - Method in class g3dsys.control.G3DSys
-
Set the min and maximum coordinates for the model.
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayBoxCanvas1D
-
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayBoxCanvas2D
-
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayPolytope
-
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayPolytopeCanvas2D
-
- setBounds(int, int, int, int) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
- setBounds(int, int, int, int) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
- setBox(Box) - Method in interface etomica.action.BoxAction
-
Specifies the Box that will be subject to the action, upon subsequent call to actionPerformed()
- setBox(Box) - Method in class etomica.action.BoxActionAdapter
-
- setBox(Box) - Method in class etomica.action.BoxQuench
-
- setBox(Box) - Method in class etomica.action.PDBWriter
-
- setBox(Box) - Method in class etomica.action.WriteConfiguration
-
Sets the box whose atom coordinates get written to the file.
- setBox(Box) - Method in class etomica.action.WriteConfigurationBinary
-
Sets the box whose atom coordinates get written to the file.
- setBox(Box) - Method in class etomica.action.WriteConfigurationDLPOLY
-
Sets the box whose atom coordinates get written to the file.
- setBox(Box) - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
Sets the box whose atom coordinates get written to the file.
- setBox(Box) - Method in class etomica.association.AtomSourceRandomDimer
-
- setBox(Box) - Method in class etomica.association.AtomSourceRandomSmer
-
- setBox(Box) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- setBox(Box) - Method in class etomica.association.BiasVolumeAceticAcid
-
- setBox(Box) - Method in class etomica.association.BiasVolumeCube
-
- setBox(Box) - Method in class etomica.association.BiasVolumeSphere
-
- setBox(Box) - Method in class etomica.association.BiasVolumeSphereOriented
-
- setBox(Box) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
- setBox(Box) - Method in class etomica.association.MCMoveBiasUB
-
- setBox(Box) - Method in class etomica.association.MCMoveBiasUBMolecule
-
- setBox(Box) - Method in class etomica.association.MCMoveDimer
-
- setBox(Box) - Method in class etomica.association.MCMoveDimerRotate
-
- setBox(Box) - Method in class etomica.association.MCMoveSmer
-
- setBox(Box) - Method in class etomica.association.MCMoveSmerRotate
-
- setBox(Box) - Method in class etomica.association.MCMoveVolumeAssociated
-
- setBox(Box) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- setBox(Box) - Method in class etomica.association.MeterDimerMoleFraction
-
- setBox(Box) - Method in class etomica.association.MoleculeSourceRandomDimer
-
- setBox(Box) - Method in interface etomica.atom.AtomSource
-
sets the Box the source should pull Atoms from.
- setBox(Box) - Method in class etomica.atom.AtomSourceRandomLeaf
-
- setBox(Box) - Method in class etomica.atom.AtomSourceRandomSpecies
-
- setBox(Box) - Method in class etomica.atom.iterator.ApiLeafAtoms
-
Conditions iterator to return all leaf-atom pairs from the given box.
- setBox(Box) - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
Sets the box containing the molecules for iteration.
- setBox(Box) - Method in class etomica.atom.iterator.AtomIteratorLeafAtoms
-
Configures iterator to form its iterates from the leaf atoms of the given
box.
- setBox(Box) - Method in interface etomica.atom.iterator.AtomsetIteratorBoxDependent
-
Sets the Box to pull iterates from
- setBox(Box) - Method in interface etomica.box.RandomPositionSource
-
Notifies the RandomPositionSource of the box from which random positions
should be taken from.
- setBox(Box) - Method in class etomica.box.RandomPositionSourceDeformable
-
- setBox(Box) - Method in class etomica.box.RandomPositionSourceRectangular
-
- setBox(Box) - Method in class etomica.data.DataProcessorInterfacialTension
-
- setBox(Box) - Method in interface etomica.data.DataSourcePositioned
-
- setBox(Box) - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
-
- setBox(Box) - Method in class etomica.data.meter.MeterAvgBondLength
-
- setBox(Box) - Method in class etomica.data.meter.MeterDensity
-
- setBox(Box) - Method in class etomica.data.meter.MeterDihedralAngle
-
- setBox(Box) - Method in class etomica.data.meter.MeterDipoleSumSquared1site
-
- setBox(Box) - Method in class etomica.data.meter.MeterDipoleSumSquaredTIP4PWater
-
- setBox(Box) - Method in class etomica.data.meter.MeterHyperVirial
-
- setBox(Box) - Method in class etomica.data.meter.MeterKineticEnergy
-
- setBox(Box) - Method in class etomica.data.meter.MeterKineticEnergyRigid
-
Sets the box to the given box.
- setBox(Box) - Method in class etomica.data.meter.MeterMoleFraction
-
- setBox(Box) - Method in class etomica.data.meter.MeterMomentumCOM
-
- setBox(Box) - Method in class etomica.data.meter.MeterNMolecules
-
- setBox(Box) - Method in class etomica.data.meter.MeterPositionCOM
-
- setBox(Box) - Method in class etomica.data.meter.MeterPotentialEnergy
-
- setBox(Box) - Method in class etomica.data.meter.MeterPressure
-
- setBox(Box) - Method in class etomica.data.meter.MeterPressureTensor
-
Sets the integrator associated with this instance.
- setBox(Box) - Method in class etomica.data.meter.MeterProfile
-
- setBox(Box) - Method in class etomica.data.meter.MeterProfileByAtoms
-
- setBox(Box) - Method in class etomica.data.meter.MeterProfileByVolume
-
- setBox(Box) - Method in class etomica.data.meter.MeterRadiusGyration
-
- setBox(Box) - Method in class etomica.data.meter.MeterRDF
-
- setBox(Box) - Method in class etomica.data.meter.MeterRDFPC
-
- setBox(Box) - Method in class etomica.data.meter.MeterTensorVelocity
-
- setBox(Box) - Method in class etomica.data.meter.MeterVolume
-
- setBox(Box) - Method in class etomica.data.meter.MeterWidomInsertion
-
- setBox(Box) - Method in class etomica.data.meter.PotentialCalculationRDF
-
- setBox(Box) - Method in class etomica.freeenergy.npath.DataSourceEnergies
-
- setBox(Box) - Method in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- setBox(Box) - Method in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- setBox(Box) - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- setBox(Box) - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- setBox(Box) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- setBox(Box) - Method in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- setBox(Box) - Method in class etomica.graphics.DeviceNSelector
-
- setBox(Box) - Method in class etomica.graphics.DisplayBox
-
Specifies the box for this display.
- setBox(Box) - Method in class etomica.integrator.IntegratorBox
-
- setBox(Box) - Method in class etomica.integrator.IntegratorConNVT
-
- setBox(Box) - Method in class etomica.integrator.IntegratorGear4
-
- setBox(Box) - Method in class etomica.integrator.IntegratorGear4NPH.ForceSumNPH
-
- setBox(Box) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setBox(Box) - Method in class etomica.integrator.IntegratorHard
-
- setBox(Box) - Method in class etomica.integrator.IntegratorMC
-
- setBox(Box) - Method in class etomica.integrator.IntegratorMD
-
- setBox(Box) - Method in class etomica.integrator.IntegratorRigidIterative
-
- setBox(Box) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- setBox(Box) - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- setBox(Box) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- setBox(Box) - Method in class etomica.integrator.IntegratorVerlet
-
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveAtom
-
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveBox
-
Sets the box on which this move acts.
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveBoxSize
-
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveDimer
-
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveManager
-
Invokes superclass method and informs all MCMoves about the new box.
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveRotate
-
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
Extends the superclass method to initialize the exchange-set species agents for the box.
- setBox(Box) - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- setBox(Box) - Method in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- setBox(Box) - Method in class etomica.liquidLJ.MeterPU
-
- setBox(Box) - Method in class etomica.liquidLJ.MeterPUCut
-
- setBox(Box) - Method in class etomica.liquidLJ.MeterPUCutLS
-
- setBox(Box) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setBox(Box) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
- setBox(Box) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- setBox(Box) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
- setBox(Box) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
-
- setBox(Box) - Method in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
- setBox(Box) - Method in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
- setBox(Box) - Method in class etomica.mappedRdf.MeterMappedRdf
-
- setBox(Box) - Method in class etomica.meam.P2EAM
-
- setBox(Box) - Method in class etomica.meam.PotentialCuLREP
-
- setBox(Box) - Method in class etomica.meam.PotentialEAM
-
- setBox(Box) - Method in class etomica.meam.PotentialEAM_LS
-
- setBox(Box) - Method in class etomica.meam.PotentialEFS
-
- setBox(Box) - Method in class etomica.meam.PotentialMEAM
-
- setBox(Box) - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- setBox(Box) - Method in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- setBox(Box) - Method in class etomica.models.co2.P2CO2H2OWheatley
-
- setBox(Box) - Method in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- setBox(Box) - Method in class etomica.models.co2.P2CO2Hellmann
-
- setBox(Box) - Method in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- setBox(Box) - Method in class etomica.models.co2.PNCO2GCPM
-
- setBox(Box) - Method in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- setBox(Box) - Method in class etomica.models.co2.PNGCPM.PNGCPMCached
-
- setBox(Box) - Method in class etomica.models.co2.PNGCPM
-
- setBox(Box) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- setBox(Box) - Method in class etomica.models.hexane.MCMoveCBMC
-
- setBox(Box) - Method in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- setBox(Box) - Method in class etomica.models.hexane.MCMoveReptate
-
- setBox(Box) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- setBox(Box) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- setBox(Box) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- setBox(Box) - Method in class etomica.models.nitrogen.P0LatticeEnergyCorrec
-
- setBox(Box) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- setBox(Box) - Method in class etomica.models.nitrogen.P2NitrogenAB
-
- setBox(Box) - Method in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- setBox(Box) - Method in class etomica.models.nitrogen.P2NitrogenShellModel
-
- setBox(Box) - Method in class etomica.models.nitrogen.PRotConstraint
-
- setBox(Box) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setBox(Box) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- setBox(Box) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- setBox(Box) - Method in class etomica.models.OPLS.P2AceticAcidTwoSite
-
- setBox(Box) - Method in class etomica.models.OPLS.P2HardAssociationRefAceticAcidTwoSite
-
- setBox(Box) - Method in class etomica.models.water.P2Water3P
-
- setBox(Box) - Method in class etomica.models.water.P2Water4P
-
- setBox(Box) - Method in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- setBox(Box) - Method in class etomica.models.water.P2WaterSzalewicz
-
- setBox(Box) - Method in class etomica.models.water.P2WaterTIP4PHardCore
-
- setBox(Box) - Method in class etomica.models.water.PNWaterGCPM.PNWaterGCPMCached
-
- setBox(Box) - Method in class etomica.models.water.PNWaterGCPM
-
- setBox(Box) - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setBox(Box) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- setBox(Box) - Method in class etomica.modules.adsorption.MyMCMove
-
- setBox(Box) - Method in class etomica.modules.adsorption.P1Wall
-
- setBox(Box) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- setBox(Box) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- setBox(Box) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- setBox(Box) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
- setBox(Box) - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
-
- setBox(Box) - Method in class etomica.modules.colloid.MeterEnd2End
-
- setBox(Box) - Method in class etomica.modules.colloid.P1Wall
-
- setBox(Box) - Method in class etomica.modules.dcvgcmd.MeterFlux
-
- setBox(Box) - Method in class etomica.modules.dcvgcmd.MyMCMove
-
- setBox(Box) - Method in class etomica.modules.droplet.IntegratorDroplet
-
- setBox(Box) - Method in class etomica.modules.droplet.MeterDeformation
-
- setBox(Box) - Method in class etomica.modules.droplet.P1Smash
-
- setBox(Box) - Method in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- setBox(Box) - Method in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- setBox(Box) - Method in class etomica.modules.entropylottery.MeterEntropy
-
- setBox(Box) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- setBox(Box) - Method in class etomica.modules.interfacial.MeterOrientation
-
- setBox(Box) - Method in class etomica.modules.materialfracture.MeterElongation
-
- setBox(Box) - Method in class etomica.modules.materialfracture.MeterStrain
-
- setBox(Box) - Method in class etomica.modules.materialfracture.MeterStress
-
- setBox(Box) - Method in class etomica.modules.materialfracture.P1Tension
-
- setBox(Box) - Method in class etomica.modules.materialfracture.StrainColorScheme
-
- setBox(Box) - Method in class etomica.modules.mu.P1MagicWall
-
- setBox(Box) - Method in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- setBox(Box) - Method in class etomica.modules.multiharmonic.MeterFreeEnergy
-
- setBox(Box) - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- setBox(Box) - Method in class etomica.modules.render.RenderMD.CriterionCar
-
- setBox(Box) - Method in class etomica.modules.rheology.MeterEndToEnd
-
- setBox(Box) - Method in class etomica.modules.rheology.MeterNormalStress
-
- setBox(Box) - Method in class etomica.modules.rheology.MeterViscosity
-
- setBox(Box) - Method in class etomica.modules.rosmosis.MeterFlux
-
- setBox(Box) - Method in class etomica.modules.sam.CriterionTether3
-
- setBox(Box) - Method in class etomica.modules.sam.MeterTilt
-
- setBox(Box) - Method in class etomica.modules.sam.MeterWallPressure
-
- setBox(Box) - Method in class etomica.modules.sam.P1Sinusoidal
-
- setBox(Box) - Method in class etomica.modules.vle.MeterPressure2
-
- setBox(Box) - Method in class etomica.molecule.iterator.MoleculeIteratorAll
-
Sets the box containing the molecules for iteration.
- setBox(Box) - Method in class etomica.molecule.iterator.MoleculeIteratorAllMolecules
-
Sets the box having the molecules to be returned as iterates.
- setBox(Box) - Method in class etomica.molecule.iterator.MoleculeIteratorMolecule
-
Sets the box containing the molecules for iteration.
- setBox(Box) - Method in interface etomica.molecule.iterator.MoleculesetIteratorBoxDependent
-
Sets the Box to pull iterates from
- setBox(Box) - Method in class etomica.molecule.iterator.MpiInterspecies1A
-
Configures iterator to return molecules from the set species in the given
box.
- setBox(Box) - Method in class etomica.molecule.iterator.MpiInterspeciesAA
-
Configures iterator to return molecules from the set species in the given
box.
- setBox(Box) - Method in class etomica.molecule.iterator.MpiIntraspecies1A
-
Configures iterator to return molecules from the set species in the given
box.
- setBox(Box) - Method in class etomica.molecule.iterator.MpiIntraspeciesAA
-
Configures iterator to return molecules from the set species in the given
box.
- setBox(Box) - Method in class etomica.molecule.iterator.MpiMolecule
-
Specifies the box from which iterates are taken.
- setBox(Box) - Method in interface etomica.molecule.MoleculeSource
-
sets the Box the source should pull Atoms from.
- setBox(Box) - Method in class etomica.molecule.MoleculeSourceRandomMolecule
-
- setBox(Box) - Method in class etomica.molecule.MoleculeToMoleculeListSpecies
-
- setBox(Box) - Method in class etomica.nbr.cell.Api1ACell
-
- setBox(Box) - Method in class etomica.nbr.cell.AtomIteratorCell
-
- setBox(Box) - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
- setBox(Box) - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
- setBox(Box) - Method in class etomica.nbr.CriterionAdapter
-
Specifies to the wrapped criterion the box where the criterion is being
applied.
- setBox(Box) - Method in class etomica.nbr.CriterionAll
-
Performs no action.
- setBox(Box) - Method in class etomica.nbr.CriterionNone
-
Performs no action.
- setBox(Box) - Method in class etomica.nbr.CriterionPositionWall
-
- setBox(Box) - Method in class etomica.nbr.CriterionSimple
-
- setBox(Box) - Method in class etomica.nbr.molecule.CriterionAdapterMolecular
-
Specifies to the wrapped criterion the box where the criterion is being
applied.
- setBox(Box) - Method in class etomica.nbr.molecule.CriterionAllMolecular
-
Performs no action.
- setBox(Box) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- setBox(Box) - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular
-
Specifies the box where the criterion is being applied.
- setBox(Box) - Method in interface etomica.nbr.NeighborCriterion
-
Specifies the box where the criterion is being applied.
- setBox(Box) - Method in class etomica.nbr.site.Api1ASite
-
- setBox(Box) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
- setBox(Box) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- setBox(Box) - Method in class etomica.normalmode.IntegratorHardMDMC
-
- setBox(Box) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveAtomSuperBox
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveHarmonicStep
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveSingleMode
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicAngle
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- setBox(Box) - Method in class etomica.normalmode.MCMoveWV
-
- setBox(Box) - Method in class etomica.normalmode.MeterAPIPotentialEnergy
-
- setBox(Box) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- setBox(Box) - Method in class etomica.normalmode.MeterNormalMode
-
Sets the box, and should be called while the Atoms are in
their lattice positions.
- setBox(Box) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setBox(Box) - Method in class etomica.normalmode.MeterPhiDeviation
-
- setBox(Box) - Method in class etomica.normalmode.MeterPlaneSlip
-
- setBox(Box) - Method in class etomica.normalmode.MeterThetaDeviation
-
- setBox(Box) - Method in class etomica.normalmode.MeterTilt
-
- setBox(Box) - Method in class etomica.normalmode.MeterTiltHistogram
-
- setBox(Box) - Method in class etomica.normalmode.MeterTiltRotation
-
- setBox(Box) - Method in class etomica.normalmode.MeterTiltRotationHistogram
-
- setBox(Box) - Method in class etomica.normalmode.MeterTiltRotationStdev
-
- setBox(Box) - Method in class etomica.normalmode.P1ConstraintNbr
-
- setBox(Box) - Method in class etomica.normalmode.P1ConstraintNbrHcp
-
- setBox(Box) - Method in class etomica.normalmode.P2XOrder
-
- setBox(Box) - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- setBox(Box) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- setBox(Box) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- setBox(Box) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- setBox(Box) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- setBox(Box) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- setBox(Box) - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- setBox(Box) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setBox(Box) - Method in class etomica.potential.EwaldSummation.P2EwaldReal
-
- setBox(Box) - Method in class etomica.potential.EwaldSummation
-
- setBox(Box) - Method in class etomica.potential.EwaldSumMolecules
-
- setBox(Box) - Method in interface etomica.potential.IPotential
-
Informs the potential of the box on which it acts so that it can
properly consider the boundaries.
- setBox(Box) - Method in class etomica.potential.P1ExternalField
-
- setBox(Box) - Method in class etomica.potential.P1HardBoundary
-
- setBox(Box) - Method in class etomica.potential.P1HarmonicSite
-
- setBox(Box) - Method in class etomica.potential.P1HydrogenMielke
-
- setBox(Box) - Method in class etomica.potential.P22CLJQ
-
- setBox(Box) - Method in class etomica.potential.P2CO2EMP
-
- setBox(Box) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- setBox(Box) - Method in class etomica.potential.P2DLPOLY
-
- setBox(Box) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
-
- setBox(Box) - Method in class etomica.potential.P2HardAssociationCone
-
- setBox(Box) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- setBox(Box) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
- setBox(Box) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
- setBox(Box) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
- setBox(Box) - Method in class etomica.potential.P2HardAssociationConeReference
-
- setBox(Box) - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
-
- setBox(Box) - Method in class etomica.potential.P2HardAssociationConeSW
-
- setBox(Box) - Method in class etomica.potential.P2HardBondedList
-
- setBox(Box) - Method in class etomica.potential.P2HardWrapper
-
- setBox(Box) - Method in class etomica.potential.P2HePCKLJS.P2HeQFH
-
- setBox(Box) - Method in class etomica.potential.P2HePCKLJS.P2HeTI
-
- setBox(Box) - Method in class etomica.potential.P2HeSimplified.P2HeQFH
-
- setBox(Box) - Method in class etomica.potential.P2HeSimplified.P2HeTI
-
- setBox(Box) - Method in class etomica.potential.P2HSDipole
-
- setBox(Box) - Method in class etomica.potential.P2HydrogenHinde
-
- setBox(Box) - Method in class etomica.potential.P2HydrogenHindeAtomic
-
- setBox(Box) - Method in class etomica.potential.P2HydrogenHindePatkowski
-
- setBox(Box) - Method in class etomica.potential.P2HydrogenHindePatkowskiAtomic
-
- setBox(Box) - Method in class etomica.potential.P2HydrogenPatkowski
-
- setBox(Box) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- setBox(Box) - Method in class etomica.potential.P2Ideal
-
Does nothing.
- setBox(Box) - Method in class etomica.potential.P2LJDipole
-
- setBox(Box) - Method in class etomica.potential.P2LJQ
-
- setBox(Box) - Method in class etomica.potential.P2LJQQ
-
- setBox(Box) - Method in class etomica.potential.P2MoleculeMonatomic
-
- setBox(Box) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- setBox(Box) - Method in class etomica.potential.P2MoleculeTruncated
-
- setBox(Box) - Method in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- setBox(Box) - Method in class etomica.potential.P2NitrogenHellmann
-
- setBox(Box) - Method in class etomica.potential.P2O2Bartolomei.P2O2TI
-
- setBox(Box) - Method in class etomica.potential.P2O2Bartolomei
-
- setBox(Box) - Method in class etomica.potential.P2QChem
-
- setBox(Box) - Method in class etomica.potential.P2ReactionFieldDipole
-
- setBox(Box) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- setBox(Box) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- setBox(Box) - Method in class etomica.potential.P2SemiclassicalAtomic
-
- setBox(Box) - Method in class etomica.potential.P2SemiclassicalMolecular
-
- setBox(Box) - Method in class etomica.potential.P2SoftSphericalTruncated
-
- setBox(Box) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- setBox(Box) - Method in class etomica.potential.P2SoftTruncated
-
- setBox(Box) - Method in class etomica.potential.P2SpheroPolyhedron
-
- setBox(Box) - Method in class etomica.potential.P2SquareWellRobust
-
- setBox(Box) - Method in class etomica.potential.P2TriangleWell
-
- setBox(Box) - Method in class etomica.potential.P2WaterPotentialsJankowski
-
- setBox(Box) - Method in class etomica.potential.P3AxilrodTeller
-
- setBox(Box) - Method in class etomica.potential.P3BondAngle
-
- setBox(Box) - Method in class etomica.potential.P3BondAngleDreiding
-
- setBox(Box) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- setBox(Box) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- setBox(Box) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setBox(Box) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- setBox(Box) - Method in class etomica.potential.P3HydrogenATM
-
- setBox(Box) - Method in class etomica.potential.P3HydrogenManzhos
-
- setBox(Box) - Method in class etomica.potential.P3Induction
-
- setBox(Box) - Method in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- setBox(Box) - Method in class etomica.potential.P4BondTorsion
-
- setBox(Box) - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- setBox(Box) - Method in class etomica.potential.P4TorsionDreiding
-
- setBox(Box) - Method in class etomica.potential.Potential
-
Informs the potential of the box on which it acts.
- setBox(Box) - Method in class etomica.potential.Potential0Lrc
-
- setBox(Box) - Method in class etomica.potential.Potential1
-
- setBox(Box) - Method in class etomica.potential.Potential2HardSpherical
-
- setBox(Box) - Method in class etomica.potential.Potential2SoftSpherical
-
- setBox(Box) - Method in class etomica.potential.Potential2SoftSphericalLS
-
- setBox(Box) - Method in class etomica.potential.PotentialAtomicSum
-
- setBox(Box) - Method in class etomica.potential.PotentialCalculationPressureTensor
-
- setBox(Box) - Method in class etomica.potential.PotentialDLPOLY
-
- setBox(Box) - Method in class etomica.potential.PotentialEmul
-
- setBox(Box) - Method in class etomica.potential.PotentialGroup
-
- setBox(Box) - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- setBox(Box) - Method in class etomica.potential.PotentialMolecular
-
Informs the potential of the box on which it acts.
- setBox(Box) - Method in class etomica.potential.PotentialMolecularMonatomic
-
- setBox(Box) - Method in class etomica.potential.PotentialMolecularSum
-
- setBox(Box) - Method in class etomica.potential.PotentialNonAdditiveDifference
-
- setBox(Box) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- setBox(Box) - Method in class etomica.rotation.P2LJDipole
-
- setBox(Box) - Method in class etomica.space.Boundary
-
Sets the box that holds the boundary.
- setBox(Box) - Method in class etomica.spin.MCMoveSpinFlip
-
- setBox(Box) - Method in class etomica.spin.MeterSpin
-
- setBox(Box) - Method in class etomica.spin.P2Spin
-
- setBox(Box) - Method in class etomica.threaded.PotentialThreaded
-
- setBox(Box) - Method in class etomica.virial.ClusterSumIC.FR2
-
- setBox(BoxCluster) - Method in interface etomica.virial.ClusterWeightSumWall.DataSourceClusterWall
-
- setBox(Box) - Method in class etomica.virial.MayerD2FDT2Spherical
-
- setBox(Box) - Method in class etomica.virial.MayerDFDTSpherical
-
- setBox(Box) - Method in class etomica.virial.MayerDFQFHDTSpherical
-
- setBox(Box) - Method in class etomica.virial.MayerEGeneral
-
- setBox(Box) - Method in class etomica.virial.MayerEHardSphere
-
- setBox(Box) - Method in class etomica.virial.MayerENonGeneral
-
- setBox(Box) - Method in class etomica.virial.MayerESpherical
-
- setBox(Box) - Method in interface etomica.virial.MayerFunction
-
- setBox(Box) - Method in class etomica.virial.MayerFunctionMolecularThreeBody
-
- setBox(Box) - Method in interface etomica.virial.MayerFunctionNonAdditive
-
- setBox(Box) - Method in class etomica.virial.MayerFunctionNonAdditiveFull
-
- setBox(Box) - Method in class etomica.virial.MayerFunctionProductGeneral
-
- setBox(Box) - Method in class etomica.virial.MayerFunctionSphericalThreeBody
-
- setBox(Box) - Method in class etomica.virial.MayerFunctionSum
-
- setBox(Box) - Method in class etomica.virial.MayerFunctionSumGeneral
-
- setBox(Box) - Method in class etomica.virial.MayerFunctionTemperature
-
- setBox(Box) - Method in class etomica.virial.MayerFunctionThreeBody
-
- setBox(Box) - Method in class etomica.virial.MayerGeneral
-
- setBox(Box) - Method in class etomica.virial.MayerGeneralAtomic
-
- setBox(Box) - Method in class etomica.virial.MayerGeneralSpherical
-
- setBox(Box) - Method in class etomica.virial.MayerHardSphere
-
- setBox(Box) - Method in class etomica.virial.MayerHSMixture
-
- setBox(Box) - Method in class etomica.virial.MayerPTAtt
-
- setBox(Box) - Method in class etomica.virial.MayerPUGeneral
-
- setBox(Box) - Method in class etomica.virial.MayerSphericalPlus
-
- setBox(Box) - Method in class etomica.virial.MayerSphericalPTAtt
-
- setBox(Box) - Method in class etomica.virial.MayerSSSeries
-
- setBox(Box) - Method in class etomica.virial.MayerWell
-
- setBox(Box) - Method in class etomica.virial.MayerXSpherical
-
- setBox(Box) - Method in class etomica.virial.MCMoveChangeBondLength
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterAngleBend
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterAtom
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterAtomDiscrete
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterAtomHSRing
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterAtomHSTree
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterAtomMulti
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterAtomQ
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterAtomRotateMulti
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterDiagram
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterMoleculeMulti
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterPolyhedraTree
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterReptateMulti
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterRingRegrow
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterRingScale
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterRotateCH3
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- setBox(Box) - Method in class etomica.virial.MCMoveClusterWiggleMulti
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterSamplingWeight
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirial
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBD
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBDBin
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalField
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldConfined
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfined
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedRho
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapConfinedSW
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldOverlapRho
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldRho
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialExternalFieldSW
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialIC
-
- setBox(BoxCluster) - Method in class etomica.virial.MeterVirialSWWE
-
- setBox(Box) - Method in class etomica.virial.MuFGeneral
-
- setBox(Box) - Method in class etomica.virial.MuGeneral
-
- setBox(Box) - Method in class etomica.virial.P1IntraLambda
-
- setBox(Box) - Method in class etomica.virial.PotentialCommonAtomic
-
- setBox(Box) - Method in class etomica.virial.PotentialEmulCached
-
- setBox(Box) - Method in class etomica.virial.PotentialGroup3PI.PotentialGroup3PISkip
-
- setBox(Box) - Method in class etomica.virial.PotentialGroup3PI
-
- setBox(Box) - Method in class etomica.virial.PotentialGroupPI.PotentialGroupPISkip
-
- setBox(Box) - Method in class etomica.virial.PotentialGroupPI
-
- setBox(Box) - Method in class etomica.virial.PotentialNonAdditive.PotentialNonAdditiveNB
-
- setBox(Box) - Method in class etomica.virial.PotentialNonAdditive
-
- setBox(Box) - Method in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.MuDeltaEBond
-
- setBox(Box) - Method in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
-
- setBox(Box) - Method in class etomica.virial.simulations.VirialB3C1TIP4Pwater.MuFBond
-
- setBox(Box) - Method in class etomica.virial.simulations.VirialB3C2TIP4Pwater.fPlusBetaEU
-
- setBox(Box) - Method in class etomica.virial.simulations.VirialB3C2TIP4Pwater.MuProduct
-
- setBox(Box) - Method in class etomica.yukawa.P2HC2Yukawa
-
- setBox(Box) - Method in class etomica.zeolite.MSDCoordWriter
-
- setBoxCanvas(DisplayCanvas) - Method in class etomica.graphics.DisplayBox
-
- setBoxFactory(SimulationVirialOverlap2.BoxClusterFactory) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setBoxIndex(int) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- setBoxSize(Box, int[]) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
Resizes simulation box to preserve periodic boundary conditions after rotation of lattice.
- setBoxSize(Vector) - Method in class etomica.space.Boundary
-
Scales the boundary dimensions such that the boundary's would be
inscribed within a rectangle of the of the given size.
- setBoxSize(Vector) - Method in class etomica.space.BoundaryDeformablePeriodic
-
Scales each boundary edge so that its length equals the corresponding value
in the given vector.
- setBoxSize(Vector) - Method in class etomica.space.BoundaryRectangular
-
Sets the size and shape of the rectangular boundary.
- setBoxSize(Vector) - Method in class etomica.space3d.BoundaryTruncatedOctahedron
-
- setBPRes(double[]) - Method in class etomica.normalmode.MeterSolidDACut
-
- setBXX(double) - Method in class etomica.models.rowley.P2RepRowley
-
- setC(double, double) - Method in class etomica.normalmode.MinimizeHCP
-
- setC(double) - Method in class etomica.potential.P2Exp6
-
- setCaching(boolean) - Method in class etomica.virial.ClusterSum
-
- setCaching(boolean) - Method in class etomica.virial.ClusterSumPolarizable
-
- setCaching(boolean) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- setCaching(boolean) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- setCapacity(int) - Method in class etomica.nbr.list.AtomNeighborLists
-
Sets the number of up and down lists maintained by this instance.
- setCapacity(int) - Method in class etomica.nbr.list.AtomPotentialList
-
- setCapacity(int) - Method in class etomica.nbr.list.molecule.MoleculeNeighborLists
-
Sets the number of up and down lists maintained by this instance.
- setCapacity(int) - Method in class etomica.nbr.list.molecule.MoleculePotentialList
-
- setCellDensity(double) - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
-
- setCellDensity(double) - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
-
- setCellDensity(double) - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
-
- setCellRange(int) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Sets the cell range to the given value.
- setCellRange(int) - Method in class etomica.nbr.cell.NeighborCellManager
-
Sets the cell range to the given value.
- setCellRange(int) - Method in class etomica.nbr.cell.PotentialMasterCell
-
- setCellRange(int) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- setCellRange(int) - Method in class etomica.nbr.list.PotentialMasterList
-
- setCellRange(int) - Method in class etomica.nbr.PotentialMasterHybrid
-
- setCellRange(int) - Method in class etomica.nbr.site.PotentialMasterSite
-
- setCellSize(double, double) - Method in class etomica.modules.sam.P1Sinusoidal
-
- setCellSizeX(double) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setCellSizeX(double) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setCellSizeZ(double) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setCellSizeZ(double) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setCenterOfRotation(Point3f) - Method in class g3dsys.control.G3DSys
-
Set the molecule space location around which rotation occurs
- setCH2element(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- setCH3element(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- setChainlength(int) - Method in class etomica.models.hexane.MCMoveCBMC
-
- setChainLength(int) - Method in class etomica.modules.colloid.ColloidSim
-
- setChainLength(int) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setChainLength(int) - Method in class etomica.modules.colloid.MeterEnd2End
-
- setChainLength(int) - Method in class etomica.modules.colloid.NeighborListManagerColloid
-
- setChainLength(int) - Method in class etomica.modules.rheology.SimulationRheology
-
- setChainLength(int) - Method in class etomica.modules.sam.Sam
-
- setChainPhi(int, double) - Method in class etomica.modules.sam.Sam
-
- setChainPsi(double) - Method in class etomica.modules.sam.Sam
-
- setChainTheta(double) - Method in class etomica.modules.sam.Sam
-
- setChangeableModes(int[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setChangeableWVs(int[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setChangeableWVs(int[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
Set the wavevectors that can be changed by the move.
- setChangeableWVs(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setCharge(double, int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setCharge(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setCharge(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setCharge1(double) - Method in class etomica.potential.P2Electrostatic
-
Sets the charge on the first type of atom.
- setCharge1(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
Sets the charge on the first type of atom.
- setCharge2(double) - Method in class etomica.potential.P2Electrostatic
-
Sets the charge on the second type of atom.
- setCharge2(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
Sets the charge on the second type of atom.
- setChildAtomTypes(int[]) - Method in class etomica.species.SpeciesSpheresCustom
-
- setChildCount(int[]) - Method in class etomica.species.SpeciesSpheresHetero
-
Directly sets the number of child atoms of each type created by this
factory.
- setCloseFileEachTime(boolean) - Method in class etomica.data.DataLogger
-
Close the file and open a new one at each time INTERVAL.
- setCloseWindow(JButton) - Method in class etomica.virial.GUI.views.ViewAlertMsgBox
-
- setCloseWindow(JButton) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- setColix(short) - Method in class org.jmol.g3d.Graphics3D
-
sets current color from colix color index
- setColix(short) - Method in class org.jmol.util.GData
-
- setColix(short) - Method in class org.jmol.util.MeshSurface
-
- setColixBack(short) - Method in class org.jmol.util.MeshSurface
-
- setCollapseOnReset(boolean) - Method in class etomica.data.history.HistoryComplete
-
Sets a flag that determines if the history is collapsed (to 100 data
points) when reset is called.
- setCollision(double, IAtom, PotentialHard) - Method in class etomica.integrator.IntegratorHard.Agent
-
Sets parameters associated with next two-body collision of this atom with another atom.
- setCollisionDiameter(double) - Method in class etomica.potential.P2HardSphere
-
Accessor method for collision diameter
- setCollisionRadius(double) - Method in class etomica.modules.osmosis.MeterOsmoticPressure
-
Sets the collision radius used to calculate accessible "area"
assuming that the relevant hard "boundaries" form right-angles with
other hard boundaries.
- setCollisionRadius(double) - Method in class etomica.modules.osmosis.P1HardWall
-
Distance from the center of the sphere to the boundary at collision.
- setCollisionRadius(double) - Method in class etomica.potential.P1HardBoundary
-
Distance from the center of the sphere to the boundary at collision.
- setCollisionRadius(double) - Method in class etomica.potential.P1HardMovingBoundary
-
Distance from the center of the sphere to the boundary at collision.
- setColloidMonomerBondManager(AtomLeafAgentManager) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setColloidSigma(double) - Method in class etomica.modules.colloid.ColloidSim
-
- setColor(char) - Method in interface etomica.graph.model.Edge
-
- setColor(char) - Method in class etomica.graph.model.impl.EdgeImpl
-
- setColor(char) - Method in class etomica.graph.model.impl.NodeImpl
-
- setColor(char) - Method in interface etomica.graph.model.Node
-
- setColor(AtomType, Color) - Method in class etomica.graphics.ColorSchemeByType
-
- setColor(AtomType, int, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeStepWise
-
Sets atoms of the given type and number of bonds to be the given color.
- setColor(String) - Method in class etomica.modules.clustergenerator.Plot
-
- setColor(short) - Method in class g3dsys.images.Axes
-
set the color of the figure
- setColor(short) - Method in class g3dsys.images.Ball
-
set the color of the figure
- setColor(short) - Method in class g3dsys.images.Box
-
set the color of the figure
- setColor(short) - Method in class g3dsys.images.Ellipse
-
set the color of the figure
- setColor(short) - Method in class g3dsys.images.Line
-
set the color of the figure
- setColor(short) - Method in class g3dsys.images.Triangle
-
set the color of the figure
- setColor(int) - Method in class org.jmol.g3d.Graphics3D
-
- setColor(int) - Method in class org.jmol.util.GData
-
- setColorIn(Color) - Method in class etomica.modules.crystalviewer.ColorSchemePlane
-
Color for atoms that are in the plane.
- setColorOut(Color) - Method in class etomica.modules.crystalviewer.ColorSchemePlane
-
Color for atoms that are out of the plane.
- setColorScheme(ConfigFromFileLAMMPS.ColorSchemeDeviation) - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- setColorScheme(ColorScheme) - Method in class etomica.graphics.DisplayBox
-
Mutator method for the color scheme used for this display
- setColumn(int, float, float, float) - Method in class org.jmol.util.Matrix3f
-
Sets the specified column of this matrix3d to the three values provided.
- setColumn(int, float[]) - Method in class org.jmol.util.Matrix4f
-
Sets the specified column of this matrix4f to the four values provided.
- setColumn4(int, float, float, float, float) - Method in class org.jmol.util.Matrix4f
-
Sets the specified column of this matrix4f to the four values provided.
- setColumnA(int, float[]) - Method in class org.jmol.util.Matrix3f
-
Sets the specified column of this matrix3d to the four values provided.
- setColumnHeader(DataTag[], String) - Method in class etomica.graphics.DisplayTable
-
- setColumnInfoFactories(DataDoubleArray.DataInfoDoubleArrayFactory[]) - Method in class etomica.data.types.DataTable.DataInfoTableFactory
-
Sets the DataInfoFactories for the columns
- setColumnNames(String[]) - Method in class etomica.graphics.DeviceTableModelGeneric
-
- setColumnV(int, Vector3f) - Method in class org.jmol.util.Matrix3f
-
Sets the specified column of this matrix3d to the vector provided.
- setCombinationProbability(double) - Method in class etomica.modules.chainequilibrium.P2SquareWellRadical
-
Sets the probability that two radicals will bond instead of becoming
unreactive.
- setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
Set the wavevectors that are removed.
- setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setComparedWV(int) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- setComparedWV(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setComponent(Object) - Method in class etomica.graphics.DeviceSlider
-
- setComponent(Object) - Method in class etomica.graphics.DeviceSpinner
-
- setComponent(int) - Method in class etomica.math.numerical.CalcGradientDifferentiable
-
- setComponent(PNCO2GCPM.Component) - Method in class etomica.models.co2.PNCO2GCPM
-
- setComponent(PNGCPM.Component) - Method in class etomica.models.co2.PNGCPM
-
- setComponent(P2WaterSzalewicz.Component) - Method in class etomica.models.water.P2WaterSzalewicz
-
- setComponent(PNWaterGCPM.Component) - Method in class etomica.models.water.PNWaterGCPM
-
- setComponent(int, int, double) - Method in interface etomica.space.Tensor
-
- setComponent(int, int, double) - Method in class etomica.space1d.Tensor1D
-
- setComponent(int, int, double) - Method in class etomica.space2d.Tensor2D
-
- setComponent(int, int, double) - Method in class etomica.space3d.Tensor3D
-
- setComponent(int, int, double) - Method in class etomica.spaceNd.TensorND
-
- setComponentValues(String[][]) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setConfigDLPOLY(WriteConfigurationDLPOLY) - Method in class etomica.potential.PotentialDLPOLY
-
- setConfigP2DLPOLY(WriteConfigurationP2DLPOLY) - Method in class etomica.potential.P2DLPOLY
-
- setConfiguration(Configuration) - Method in class etomica.action.SimulationRestart
-
- setConfiguration(Configuration) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setConfiguration(Configuration) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setConfiguration(Configuration) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- setConfiguration(Configuration) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- setConfName(String) - Method in class etomica.action.WriteConfiguration
-
Sets the configuration name.
- setConfName(String) - Method in class etomica.action.WriteConfigurationBinary
-
Sets the configuration name.
- setConfName(String) - Method in class etomica.action.WriteConfigurationDLPOLY
-
Sets the configuration name.
- setConfName(String) - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
Sets the configuration name.
- setConformation(IConformation) - Method in class etomica.chem.models.ModelChain
-
Sets the Conformation for the molecule.
- setConformation(int, ConformationChainZigZag) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setConformation(IConformation) - Method in class etomica.species.Species
-
- setConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setConformation() - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setConformationParameters(double, double) - Method in class etomica.virial.SpeciesAlkane
-
- setConstrainScriptOrigin(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets whether scripts should only be loaded from the same
location as the documents referencing them.
- setConstraint(IPotentialAtomic) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterDDP
-
- setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterDP
-
- setConstraint(P1ConstraintNbr) - Method in class etomica.normalmode.MeterTargetTP
-
- setConstraintAngle(double) - Method in class etomica.models.nitrogen.MeterDirectInitPert
-
- setConstraintAngle(double) - Method in class etomica.models.nitrogen.PRotConstraint
-
- setConstraintMap(int[]) - Method in class etomica.virial.MCMoveClusterMoleculeMulti
-
- setConstraintMap(int[]) - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- setConstructorObject(Integer) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setContainingCubeEdgeLength(double) - Method in class etomica.math.geometry.TruncatedOctahedron
-
Sets the size of the truncated octahedron in terms of the edge length of
a cube that would contain it.
- setController(Controller) - Method in interface etomica.action.ControllerAction
-
- setController(Controller) - Method in class etomica.action.ControllerActionAdapter
-
- setController(Controller) - Method in class etomica.graphics.Device
-
- setController(Controller) - Method in class etomica.graphics.DeviceControllerButton
-
- setController(Controller) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the temperature slider controller.
- setController(Controller) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the temperature slider controller.
- setController(Controller) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the n- Cell # slider controller.
- setController(Controller) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the x- and y- Cell # slider controller.
- setController(Controller) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the eigenvalue # slider controller.
- setController(Controller) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the wavevector # slider controller.
- setConvertedWV(int) - Method in class etomica.models.oneDHardRods.MeterF
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.conjugategradient.DerivativeEnergyFunction
-
- setCoordinateDefinition(CoordinateDefinitionNitrogen) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.CalcJacobian
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveHarmonicStep
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MCMoveSingleMode
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterDDP
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterDP
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterNormalMode
-
Sets the object that defines the real-space generalized coordinates.
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.normalmode.MeterTargetTP
-
- setCoordinateDefinition(CoordinateDefinitionParacetamol) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setCoordinateDefinition(CoordinateDefinition) - Method in class etomica.paracetamol.NumericalDerivativeEnergyParacetamol
-
- setCoordinateDefinitionParacetamol(CoordinateDefinitionParacetamol) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
- setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2DoubleWell
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2PenetrableSphere
-
Mutator method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2PenetrableSquareWell
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2SquareWell
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2SquareWellRobust
-
Accessor method for core diameter.
- setCoreDiameter(double) - Method in class etomica.potential.P2TriangleWell
-
- setCoreDiameterSquared(double) - Method in class etomica.potential.P2PenetrableSquareWell
-
- setCountOfMoleculesStrings(String[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setCountOfSpeciesSLM(SpinnerListModel, int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setCountOfSpeciesSLMListener(ChangeListener[]) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setCountSpecies(int, int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setCoupling(double) - Method in class etomica.spin.P2Spin
-
- setCriterion(IPotentialMolecular, NeighborCriterionMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Sets the criterion associated with the given potential, overriding the
default provided by the PotentialMasterList.
- setCriterion(IPotentialAtomic, NeighborCriterion) - Method in class etomica.nbr.list.PotentialMasterList
-
Sets the criterion associated with the given potential, overriding the
default provided by the PotentialMasterList.
- setCriterion(IPotentialAtomic, NeighborCriterion) - Method in class etomica.nbr.site.PotentialMasterSite
-
Sets the criterion associated with the given potential, overriding the
default provided by the PotentialMasterCell.
- setCriterion(IPotential, NeighborCriterion) - Method in class etomica.potential.PotentialArray
-
Sets the criterion associated with the given potential
- setCriterion(IPotentialMolecular, NeighborCriterionMolecular) - Method in class etomica.potential.PotentialArrayMolecular
-
Sets the criterion associated with the given potential
- setCSPotential(P2SquareWellSurface) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- setCubicSize(double) - Method in class etomica.lattice.crystal.PrimitiveBcc
-
Sets the length of all primitive vectors to the given value.
- setCubicSize(double) - Method in class etomica.lattice.crystal.PrimitiveFcc
-
Sets the length of all primitive vectors to the given value.
- setCubicSize(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
Sets the length of all primitive vectors to the given value.
- setCursor(int, Object) - Method in interface org.jmol.api.ApiPlatform
-
- setCursor(int, Object) - Method in class org.jmol.awt.Platform
-
- setCutoff(double) - Method in class etomica.data.meter.MeterStructureFactor
-
Sets the wave vector cutoff.
- setCutoff(double, double) - Method in class etomica.meam.P2EAM
-
- setCutoff(double) - Method in class etomica.modules.droplet.AtomFilterLiquid
-
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffFactorLJ(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for Lennard-Jones cutoff distance; divided by sigma
- setCutoffRatio(double) - Method in class etomica.potential.P2MoleculeTruncated
-
- setCutoffRatio(double) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- setCVector(Vector) - Method in class etomica.action.BoxInflateAnisotropic
-
- setCXX(double) - Method in class etomica.models.rowley.P2RepRowley
-
- setD(float) - Method in class g3dsys.images.Ball
-
set the molspace diameter of the figure, when applicable
- setD(float) - Method in class g3dsys.images.Bond
-
set the molspace diameter of the figure, when applicable
- setD(float) - Method in class g3dsys.images.Ellipse
-
set the molspace diameter of the figure, when applicable
- setD2dfac(double) - Method in class etomica.math.numerical.AkimaSplineSmoother
-
sets weight given to minimizing discontinuities in the 2nd derivative
(at data points)
- setD2fac(double) - Method in class etomica.math.numerical.AkimaSplineSmoother
-
sets weight given to minimizing the 2nd derivative
- setD3dfac(double) - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- setD3fac(double) - Method in class etomica.math.numerical.AkimaSplineSmoother
-
sets weight given to minimizing the 3nd derivative
- setDampingParams(int, int, double, int, boolean) - Method in class etomica.potential.P2QChemInterpolated
-
The energy u.
- setData(double[], double[]) - Method in class etomica.math.numerical.FastFourierTransform
-
Saves the two passed arrays of doubles into this class, real and
imaginary in order to transform.
- setData(double[], boolean) - Method in class etomica.math.numerical.FastFourierTransform
-
For passing only all reals (true) or all imaginaries (false)
- setData(double[]) - Method in class etomica.math.numerical.FastFourierTransform
-
For passing only one set of data - assumes passing all reals
- setData(int, double) - Method in class etomica.modules.statistics.DataCollector
-
- setData(IData) - Method in class etomica.server.representations.DataAndInfo
-
- setDataInfo(IDataInfo) - Method in class etomica.server.representations.DataAndInfo
-
- setDataResetAction(SimulationDataAction) - Method in class etomica.action.SimulationRestart
-
- setDataSink(int, IDataSink) - Method in class etomica.data.DataDistributer
-
Sets the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
- setDataSink(IDataSink) - Method in class etomica.data.DataFork
-
Sets the given DataSink as the only one connected to this DataFork.
- setDataSink(int, IDataSink) - Method in class etomica.data.DataGroupSplitter
-
Sets the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
- setDataSink(IDataSink) - Method in class etomica.data.DataLogger
-
- setDataSink(IDataSink) - Method in interface etomica.data.DataPipe
-
Sets the DataSink that will receive data from this DataPipe.
- setDataSink(IDataSink) - Method in class etomica.data.DataProcessor
-
Sets the sink receiving the data.
- setDataSink(IDataSink) - Method in class etomica.data.DataProcessorForked
-
- setDataSink(int, IDataSink) - Method in class etomica.data.DataSplitter
-
Sets the DataSink for the ith output stream (corresponding to the ith
numerical value coming in).
- setDataSinkFactory(DataSplitter.IDataSinkFactory) - Method in class etomica.data.DataSplitter
-
- setDataSinks(IDataSink[]) - Method in class etomica.data.DataFork
-
- setDataSinks(IDataSink[]) - Method in interface etomica.data.DataPipeForked
-
Sets the list of DataSinks that receive the Data entering this DataFork.
- setDataSinks(IDataSink[]) - Method in class etomica.data.DataProcessorForked
-
- setDataSource(DataSourcePositioned) - Method in class etomica.data.meter.MeterProfile
-
Accessor method for the meter that defines the profiled quantity.
- setDataSource(DataSourceMolecular) - Method in class etomica.data.meter.MeterProfileByAtoms
-
Accessor method for the meter that defines the profiled quantity.
- setDataSource(DataSourceMolecular) - Method in class etomica.data.meter.MeterProfileByVolume
-
Accessor method for the meter that defines the profiled quantity.
- setDataSourceA(DataSourceScalar) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
- setDataSourceB(DataSourceScalar) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
- setDataSourceMuRoot(DataSourceMuRoot) - Method in class etomica.normalmode.DataSourceAvgPressure2
-
- setDecimalMode() - Method in class etomica.util.ScientificFormat
-
- setDecimalSeparatorAlwaysShown(boolean) - Method in class etomica.util.ScientificFormat
-
- setDecimalSliderLabelTable(Hashtable) - Method in class etomica.graphics.DecimalSlider
-
- setDecimalSliderMajorTickSpacing(double) - Method in class etomica.graphics.DecimalSlider
-
- setDecimalSliderMaximum(double) - Method in class etomica.graphics.DecimalSlider
-
- setDecimalSliderMinimum(double) - Method in class etomica.graphics.DecimalSlider
-
- setDecimalSliderMinorTickSpacing(double) - Method in class etomica.graphics.DecimalSlider
-
- setDecimalSliderValue(double) - Method in class etomica.graphics.DecimalSlider
-
- setDefaultColor(Color) - Method in class etomica.graphics.ColorScheme
-
- setDefaultDaDef(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- setDefaultFontFamily(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the defaultFontFamily value.
- setDefaultLabel(String) - Method in class etomica.graphics.DisplayTextBox
-
Sets label to the given value if it was not previously set.
- setDefaultRotation() - Method in class g3dsys.control.G3DSys
-
Rescales slab and depth after image shell mode is toggled
or the number of layers changed.
- setDeformation(double) - Method in class etomica.modules.droplet.ConfigurationDroplet
-
- setDegeneracy(int[]) - Method in class etomica.math.discrete.PermutationDegenerateIterator
-
Invokes setDegeneracy(degeneracy, degeneracy.length), thus using all elements of given array.
- setDegeneracy(int[], int) - Method in class etomica.math.discrete.PermutationDegenerateIterator
-
Sets parameter that describes number of duplicate elements in the
iterates.
- setDelayExponent(double) - Method in class etomica.graphics.DeviceDelaySlider
-
- setDeltaCut(double) - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizable
-
- setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- setDeltaCut(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- setDeltaTmax(int) - Method in class etomica.zeolite.MSDProcessor
-
Allows for a new value of deltaTmax.
- setDeltaX(double) - Method in class etomica.data.histogram.HistogramExpanding
-
- setDenominator(int) - Method in interface etomica.graph.model.Coefficient
-
- setDenominator(int) - Method in class etomica.graph.model.impl.CoefficientImpl
-
- setDensity(double) - Method in class etomica.box.Box
-
Uses BoxInflate to adjust the volume to the specified density.
- setDensityProfileDump(IDataSource) - Method in class etomica.data.DataProcessorChemicalPotential
-
- setDepth(double) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Set depth percentage
- setDepth(double) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Set depth percentage
- setDepth(int) - Method in class org.jmol.util.GData
-
clipping from the front and the back
- setDepthPercent(float) - Method in class g3dsys.control.G3DSys
-
- setDescription(JTextArea) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setDescription(JTextArea) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setDestination(Vector) - Method in class etomica.action.MoleculeActionTranslateTo
-
- setDestinationType(DestinationType) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the destinationType attribute value.
- setDiagram(int) - Method in class etomica.virial.ClusterSumStickyEF
-
- setDiagramSampling(boolean) - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- setDiameter(String, double) - Method in class etomica.atom.DiameterHashByElement
-
- setDiameter(String, double) - Method in class etomica.atom.DiameterHashByElementType
-
- setDiameter(AtomType, double) - Method in class etomica.atom.DiameterHashByType
-
- setDiameterHash(DiameterHash) - Method in class etomica.graphics.DisplayBox
-
Sets the DiameterHash used by this DisplayBox.
- setDielectric(double) - Method in class etomica.potential.P2ReactionFieldDipole
-
- setDielectric(double) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
Sets the dielectric constant of the fluid surrounding the cavity.
- setDiffusePercent(int) - Static method in class org.jmol.util.GData
-
df in I = df * (N dot L) + sf * (R dot V)^p
- setDim(Dimension) - Method in class etomica.units.gui.UnitGraphics
-
- setDimension(Dimension) - Method in class etomica.data.DataInfoFactory
-
Sets the dimension
- setDimension(Dimension) - Method in interface etomica.data.IDataInfoFactory
-
Sets the dimension
- setDimensions(int, int, int, int, int, int, double, double, double, double, double, double) - Method in class etomica.config.GrainBoundaryConfiguration
-
- setDimensions(Vector) - Method in class etomica.lattice.CellLattice
-
- setDimensions(Tensor) - Method in class etomica.space.BoundaryDeformablePeriodic
-
Sets the boundary tensor to equal the given tensor.
- setDims(int[]) - Method in class etomica.modules.rheology.MeterNormalStress
-
- setDimx(int) - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- setDimy(int) - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- setDipole(double) - Method in class etomica.potential.P2HSDipole
-
- setDipole(double) - Method in class etomica.potential.P2LJDipole
-
- setDipoleMomentSquare(double) - Method in class etomica.rotation.P2LJDipole
-
- setDipoleSource(DipoleSource) - Method in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- setDipoleSource(DipoleSource) - Method in class etomica.potential.P1ExternalField
-
- setDipoleSource(DipoleSource) - Method in class etomica.potential.P2ReactionFieldDipole
-
- setDipoleSource(DipoleSource) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
Sets the dipole source used by this object should use.
- setDipoleSource(DipoleSource) - Method in class etomica.potential.PotentialCalculationPhiSum
-
- setDipoleStrength(double) - Method in class etomica.models.water.DipoleSourceWater
-
Sets the strength (magnitude) of the dipole.
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.ApiIntragroup
-
Specifies the direction, which applies only if iterating pairs
with a target atom; otherwise, if all pairs from group are indicated,
direction is ignored.
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
Has no effect, but is included as part of the AtomsetIteratorPDT interface.
- setDirection(IteratorDirective.Direction) - Method in interface etomica.atom.iterator.AtomsetIteratorDirectable
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.atom.iterator.TripletInnerSequential
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Sets the iterator to return only up-list neighbors or down-list neighbors.
- setDirection(IteratorDirective.Direction) - Method in class etomica.molecule.iterator.MoleculeIteratorAll
-
Has no effect, but is included as part of the AtomsetIteratorPDT interface.
- setDirection(IteratorDirective.Direction) - Method in class etomica.molecule.iterator.MoleculeIteratorMolecule
-
Has no effect, but is included as part of the AtomsetIteratorPDT interface.
- setDirection(IteratorDirective.Direction) - Method in class etomica.molecule.iterator.MpiInterspecies1A
-
Indicates allowed direction for iteration, relative to specified target
atom.
- setDirection(IteratorDirective.Direction) - Method in class etomica.molecule.iterator.MpiIntraspecies1A
-
Specifies the direction, which applies only if iterating pairs
with a target atom; otherwise, if all pairs from group are indicated,
direction is ignored.
- setDirection(IteratorDirective.Direction) - Method in class etomica.molecule.iterator.MpiMolecule
-
Specifies the direction from which partners of a target atoms
are taken to form iterates.
- setDirection(IteratorDirective.Direction) - Method in class etomica.nbr.cell.Api1ACell
-
Indicates allowed direction for iteration, relative to specified target
atom.
- setDirection(IteratorDirective.Direction) - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
Indicates allowed direction for iteration, relative to specified target
atom.
- setDirection(IteratorDirective.Direction) - Method in class etomica.nbr.site.Api1ASite
-
Indicates allowed direction for iteration, relative to specified target
atom.
- setDirection(IteratorDirective.Direction) - Method in class etomica.potential.IteratorDirective
-
- setDirection(IteratorDirective.Direction) - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- setDirection(Vector) - Method in interface etomica.space.IOrientation
-
Sets this orientation to point in the given direction.
- setDirection(Vector) - Method in class etomica.space1d.Orientation1D
-
- setDirection(Vector) - Method in class etomica.space2d.Orientation2D
-
- setDirection(Vector) - Method in class etomica.space3d.Orientation3D
-
Sets this orientation to point in the given direction.
- setDirection(Vector) - Method in class etomica.space3d.OrientationFull3D
-
Sets this orientation to point in the given direction.
- setDirection(Vector) - Method in class etomica.spin.P1MagneticField
-
- setDirections(Vector, Vector) - Method in interface etomica.space3d.IOrientationFull3D
-
Sets the orientation's primary and secondary direction to be the given
directions.
- setDirections(Vector, Vector) - Method in class etomica.space3d.OrientationFull3D
-
- setDisp(boolean) - Method in class etomica.potential.P2QChemInterpolated
-
- setDisplayDensity(double) - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- setDisplayDensity(double) - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- setDisplayDensity(double) - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- setDistanceToOrigin(double) - Method in class etomica.math.geometry.Plane
-
Sets perpendicular distance from the plane to the origin.
- setDoAdjustOnTime(boolean) - Method in class etomica.overlap.IntegratorOverlap
-
If true, causes the integrator to optimize how much each system runs
based on the wall clock time needed to run steps in each system.
- setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfiguration
-
Directs the writer to apply periodic boundary conditions or not (true
by default).
- setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfigurationBinary
-
Directs the writer to apply periodic boundary conditions or not (true
by default).
- setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfigurationDLPOLY
-
Directs the writer to apply periodic boundary conditions or not (true
by default).
- setDoApplyPBC(boolean) - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
Directs the writer to apply periodic boundary conditions or not (true
by default).
- setDoApplyPBC(boolean) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- setDoApplyPBC(boolean) - Method in class etomica.nbr.cell.NeighborCellManager
-
- setDoApplyPBC(boolean) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- setDoApplyPBC(boolean) - Method in class etomica.nbr.list.NeighborListManager
-
- setDoAveraging(boolean) - Method in class etomica.data.histogram.HistogramNotSoSimple
-
turns "averaging" on or off.
- setDoCaching(boolean) - Method in class etomica.virial.ClusterWheatleySoft
-
- setDoCaching(boolean) - Method in class etomica.virial.ClusterWheatleySoftBD
-
- setDoCaching(boolean) - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
- setDoCaching(boolean) - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- setDoClear(boolean) - Method in class etomica.graphics.DisplayPlot
-
- setDoConfigButton(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
Enable the config (and velocity) buttons.
- setDoCov(boolean) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- setDoDensityInput(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
Enable the RDF plot.
- setDoDisconnectedMatching(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoDisconnectedMatching(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- setDoDisconnectedMatching(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoDouble(boolean) - Method in class etomica.modules.rheology.MeterNormalStress
-
- setDoDrawLines(DataTag[], boolean) - Method in class etomica.graphics.DisplayPlot
-
Sets the data set corresponding to the given tags to be have the data
points connected with lines or not.
- setDoEnforceBounds(boolean) - Method in class etomica.data.DataSourceUniform
-
- setDoExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoExchange(boolean[]) - Method in class etomica.virial.MCMoveChangeBondLength
-
- setDoExchange(boolean[]) - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
- setDoExchangeCondensing(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
Turn on replacement of exchanged groups of nodes with a single node (of
a different color)
- setDoExchangeCondensing(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
Turn on replacement of exchanged groups of nodes with a single node (of
a different color)
- setDoExchangeF(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
Turn on replacement of eBonds with bonds that represent a single fBond
between an exchange group and another molecule (or another exchange
group).
- setDoExchangeF(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
Turn on replacement of eBonds with bonds that represent a single fBond
between an exchange group and another molecule (or another exchange
group).
- setDoExcludeBogusConfigs(boolean) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- setDoExcludeBogusConfigs(boolean) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- setDoExcludeNonNeighbors(boolean) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
Configures the move to not explicitly calculate the potential for atom
pairs that are not neighbors (as determined by the potentialMaster).
- setDoExcludeNonNeighbors(boolean) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
Configures the move to not explicitly calculate the potential for atom
pairs that are not neighbors (as determined by the potentialMaster).
- setDoExcludeNonNeighbors(boolean) - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
Configures the move to not explicitly calculate the potential for atom
pairs that are not neighbors (as determined by the potentialMaster).
- setDoExp(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoFastButton(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- setDoHB(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
Enable construction of diagrams from the Hellmann-Bich formulation
- setDoHB(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
Enable construction of diagrams from the Hellmann-Bich formulation
- setDoIncludeCoefficients(boolean) - Method in class etomica.graph.viewer.GraphMap
-
- setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- setDoKeepEBonds(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoLegend(boolean) - Method in class etomica.graphics.DisplayPlot
-
Mutator for flag determining if a legend is to be shown.
- setDoMinimalBC(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoMinimalBC(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- setDoMinimalBC(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoMinimalMulti(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
Only include graphs with nonadditive bonds.
- setDoMinimalMulti(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- setDoMinimalMulti(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoMultiFromPair(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoMultiFromPair(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoNegativeExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoNegativeExchange(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoNMoleculeSlider(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
Enable the # of molecules slider.
- setDoNonEquilibrium(boolean) - Method in class etomica.potential.PotentialCalculationPressureTensor
-
- setDoPBC(boolean) - Method in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
-
- setDoPBC(boolean) - Method in class etomica.models.nitrogen.BoundaryRectangularPeriodicSwitch
-
- setDoPrevious(boolean) - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- setDoRDF(boolean) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
Enable the RDF plot.
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoReeHoover(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- setDoResetFilter(boolean) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- setDoScaling(boolean) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setDoSecondDerivative(boolean) - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram1qbond
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram2qbonds
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.MayerIonicDiagram4qbonds
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- setDoShortcut(boolean) - Method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- setDoShowCurrent(boolean) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- setDoStrictBlockData(boolean) - Method in class etomica.data.AccumulatorAverageFixed
-
Sets the accumulator to base statistics only on block data (where that
makes sense).
- setDoWiggle(boolean) - Method in class etomica.virial.simulations.SimulationVirial
-
- setDoWiggle(boolean) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setDrawable(boolean) - Method in class g3dsys.images.Figure
-
- setDrawable(boolean) - Method in class g3dsys.images.ImageShell
-
- setDrawBoundary(int) - Method in class etomica.graphics.DisplayCanvas
-
- setDrawBoundaryType(int) - Method in class g3dsys.images.ImageShell
-
Sets the boundary drawing style
- setDrawingHeight(int) - Method in class etomica.graphics.DisplayBox
-
Set the height of the drawing area (only relevant for 1D)
- setDrawingThickness(int) - Method in class etomica.potential.P1HardBoundary
-
- setDrawNumbersOfBlack(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
-
- setDrawNumbersOfWhite(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
-
- setDrawOverflow(boolean) - Method in class etomica.graphics.DisplayBox
-
- setDrawPoints(boolean) - Method in class etomica.modules.clustergenerator.MyApplet.Starter
-
- setDsABase(double) - Method in class etomica.models.oneDHardRods.MeterOverlap
-
- setDsABase(double) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
- setDsBBase(double) - Method in class etomica.models.oneDHardRods.MeterOverlap
-
- setDsBBase(double) - Method in class etomica.models.oneDHardRods.MeterOverlapSameGaussian
-
- setDst(File) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
When converting a single source, dst can be a file.
- setDSVO(DataSourceVirialOverlap) - Method in class etomica.virial.overlap.IntegratorOverlap
-
Sets the DataSource that retrieves data from both boxs and provides
information to the integrator about their progress.
- setDv(double) - Method in class etomica.modules.droplet.P2Cohesion
-
- setEdgeLength(double) - Method in class etomica.math.geometry.Cube
-
- setEdgeLength(double) - Method in class etomica.math.geometry.Square
-
- setEdgeLength(double) - Method in class etomica.math.geometry.TruncatedOctahedron
-
Specifies the common length of all edges of the truncated octahedron.
- setEdgeLengths(Vector) - Method in class etomica.math.geometry.Cuboid
-
Sets the three edge lengths of the cuboid, taking
each element of the given vector for the length of
the corresponding cuboid edge.
- setEdgeLengths(double, double, double) - Method in class etomica.math.geometry.Cuboid
-
Sets the lengths of all edges of the cuboid.
- setEdgeLengths(Vector) - Method in class etomica.math.geometry.LineSegment
-
Sets the length equal to the element of the (presumably 1D) vector.
- setEdgeLengths(Vector) - Method in class etomica.math.geometry.Rectangle
-
Sets the two edge lengths of the rectangle, taking
each element of the given vector for the length of
the corresponding rectangle edge.
- setEdgeLengths(double, double) - Method in class etomica.math.geometry.Rectangle
-
- setEdgeLengths(Vector) - Method in interface etomica.math.geometry.Rectangular
-
Specifies the D edge lengths needed to describe the shape
of the polytope.
- setEdgeVector(int, Vector) - Method in class etomica.space.BoundaryDeformablePeriodic
-
- setEdgeVectors(Vector[]) - Method in class etomica.math.geometry.Parallelepiped
-
Sets the lengths and directions of all edges of the parellelepiped.
- setEdgeVectors(Vector[]) - Method in class etomica.math.geometry.Parallelogram
-
Sets the lengths and directions of all edges of the parellelepiped.
- setEdgeVectors(Vector[]) - Method in interface etomica.math.geometry.Parallelotope
-
Specifies the polytope via an array of edge vectors.
- setEditable(boolean) - Method in class etomica.graphics.DeviceBox
-
- setEditValues(boolean) - Method in class etomica.graphics.DeviceSlider
-
- setEditValues(boolean) - Method in class etomica.graphics.DeviceThermoSlider
-
Set whether the temperature text box should be editable.
- setEditValues(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set whether the temperature text box should be editable.
- setEditValues(boolean) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set whether the x- and y-Cell # text box should be editable.
- setEditValues(boolean) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set whether the eigenvalue # text box should be editable.
- setEditValues(boolean) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set whether the wavevector # text box should be editable.
- setEditVariables(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setEditVariables(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
Informs the move of the eigenvectors for the selected wave vector.
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
Informs the move of the eigenvectors for the selected wave vector.
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
Informs the move of the eigenvectors
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterF
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setEigenVectors(double[][][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setEigenVectors(double[][][]) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setEigenVectors(double[][][]) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setEigenVectors(double[][]) - Method in class etomica.normalmode.MCMoveHarmonicStep
-
Informs the move of the eigenvectors for the k=0 wave vector.
- setEigenVectors(double[][][]) - Method in class etomica.normalmode.MCMoveSingleMode
-
Informs the move of the eigenvectors for the selected wave vector.
- setEigenvectors(double[]) - Method in class etomica.normalmode.MeterHarmonicCoordinate
-
- setEigenvectors(double[][][]) - Method in class etomica.normalmode.MeterHarmonicEnergy
-
- setEigenvectors(double[][][]) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- setElement(IElement) - Method in class etomica.chem.models.ModelChain
-
Sets the Element used for the leaf atoms in the chain.
- setElement(int, int, float) - Method in class org.jmol.util.Matrix3f
-
Sets the specified element of this matrix3d to the value provided.
- setElement(int, int, float) - Method in class org.jmol.util.Matrix4f
-
Sets the specified element of this matrix4f to the value provided.
- setEllipsoidMatrix(Vector3f[], float[], Vector3f, Matrix3f) - Static method in class org.jmol.util.Quadric
-
- setEnabled(boolean) - Method in class etomica.graphics.DeviceNSelector
-
- setEnabled(boolean) - Method in class etomica.graphics.DeviceSlider
-
Sets the deivce's slider and textfield to be enabled or not.
- setEnabled(IPotentialAtomic, boolean) - Method in class etomica.potential.PotentialGroup
-
Indicates that the specified potential should not contribute to potential
calculations.
- setEnabled(boolean) - Method in class etomica.potential.PotentialMaster
-
Permits enabling/disabling of all potentials.
- setEnabled(IPotentialMolecular, boolean) - Method in class etomica.potential.PotentialMaster
-
Indicates that the specified potential should not contribute to potential
calculations.
- setEnabled(IPotentialAtomic, boolean) - Method in class etomica.potential.PotentialMaster
-
Indicates that the specified potential should not contribute to potential
calculations.
- setEnabled(boolean) - Method in class etomica.potential.PotentialMasterLrc
-
- setEnabled(boolean) - Method in class etomica.util.Grabber.ActionCornerSetter
-
- setEnabled(boolean) - Method in class etomica.util.Grabber.DefaultMouseListener
-
- setEnablePBC(boolean) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- setEnd(Point3f) - Method in class g3dsys.images.Line
-
- setEnd(float, float, float) - Method in class g3dsys.images.Line
-
- setEnergyBase(double) - Method in class etomica.normalmode.BoltzmannProcessor
-
- setEnergyFac(double) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingRegrow
-
sets the harmonic bond "energy" factor
The probability of the bond have length x is proportional to exp(-factor*x^2)
(there is no temperature involved here)
- setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
sets the harmonic bond "energy" factor
The probability of the bond to have length x is proportional to exp(-factor*x^2)
(there is no temperature involved here)
- setEnergyFactor(double) - Method in class etomica.virial.MCMoveClusterRingScale
-
- setEnergyMeter(MeterPotentialEnergy) - Method in class etomica.data.meter.MeterWidomInsertion
-
- setEnergyMeter(MeterPotentialEnergy, MeterPotentialEnergy) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setEnergyMeter(MeterPotentialEnergy) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
- setEpsilon(double) - Method in class etomica.modules.adsorption.EOSSW
-
- setEpsilon(double) - Method in class etomica.modules.adsorption.P1Wall
-
- setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.modules.colloid.P1Wall
-
- setEpsilon(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- setEpsilon(double) - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
- setEpsilon(double) - Method in class etomica.modules.droplet.P2Cohesion
-
- setEpsilon(double) - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.modules.render.RenderMD.P2PenetrableCar
-
- setEpsilon(double) - Method in class etomica.modules.rosmosis.P1Tether
-
- setEpsilon(double) - Method in class etomica.modules.sam.P1WCAWall
-
- setEpsilon(double) - Method in class etomica.modules.vle.VLESim
-
- setEpsilon(double) - Method in class etomica.potential.P22CLJQ
-
- setEpsilon(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociation
-
Accessor method for depth of well.
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2LennardJones
-
Mutator method for Lennard-Jones energy parameter
- setEpsilon(double) - Method in class etomica.potential.P2LennardJonesDreiding
-
Mutator method for Lennard-Jones energy parameter
- setEpsilon(double) - Method in class etomica.potential.P2LJDipole
-
- setEpsilon(double) - Method in class etomica.potential.P2LJQ
-
- setEpsilon(double) - Method in class etomica.potential.P2LJQQ
-
- setEpsilon(double) - Method in class etomica.potential.P2ModifiedMorse
-
- setEpsilon(double) - Method in class etomica.potential.P2Morse
-
- setEpsilon(double) - Method in class etomica.potential.P2PenetrableSphere
-
Accessor method for height of core.
- setEpsilon(double) - Method in class etomica.potential.P2PenetrableSquareWell
-
Mutator method for depth of well.
- setEpsilon(double) - Method in class etomica.potential.P2SoftSphere
-
Mutator method for soft-sphere energy parameter
- setEpsilon(double) - Method in class etomica.potential.P2SquareWell
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2SquareWellRobust
-
Accessor method for depth of well
- setEpsilon(double) - Method in class etomica.potential.P2TriangleWell
-
- setEpsilon(double) - Method in class etomica.potential.P2WCA
-
Mutator method for the energy parameter
- setEpsilon(double) - Method in class etomica.potential.P3BondAngle
-
Sets the characteristic energy of the potential
- setEpsilon(double) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
Sets the characteristic energy of the potential
- setEpsilon(double) - Method in class etomica.rotation.P2LJDipole
-
- setEpsilon(double) - Method in class etomica.units.systems.LJ
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setEpsilon(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setEpsilon(double) - Method in class etomica.yukawa.P2HC2Yukawa
-
Mutator methods for size and energy parameters.
- setEpsilon6(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setEpsilonBonding(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- setEpsilonBonding(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- setEpsilonCG(double) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- setEpsilonCore(double) - Method in class etomica.potential.P2DoubleWell
-
Accessor method for depth of well
- setEpsilonCore(double) - Method in class etomica.potential.P2PenetrableSquareWell
-
Sets height of penetrable core.
- setEpsilonNR(double) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- setEpsilonWell(double) - Method in class etomica.potential.P2DoubleWell
-
- setEpsInner(double) - Method in class etomica.potential.P2PenetrableBond
-
- setEpsOuter(double) - Method in class etomica.potential.P2PenetrableBond
-
- setEquilibrating(boolean) - Method in class etomica.integrator.mcmove.MCMoveManager
-
- setErrMulti(double) - Method in class etomica.potential.P2HePCKLJS
-
- setEthanolParams(int) - Static method in class etomica.models.rowley.EthanolRouteParams
-
- setEValNum(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the current value for the eigenvalue # slider/text box.
- setEValNum(int) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setEventInterval(int) - Method in class etomica.integrator.Integrator
-
Sets value of interval between successive firing of integrator interval events.
- setExcludeArticulationPair(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to exclude clusters having an articulation pair.
- setExcludeArticulationPoint(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to exclude clusters having an articulation point.
- setExcludeNodalPoint(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to exclude clusters having a nodal point.
- setExecuteOnload(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets whether or not scripts attached to the DOM using 'onload'
event attribute must be executed before rasterizing.
- setExp(int) - Method in class etomica.virial.MayerSSSeries
-
Sets the HS diameter.
- setExpGroupingSize(int) - Method in class etomica.util.ScientificFormat
-
- setExpMaximumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
-
- setExpMinimumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
-
- setExpNegativePrefix(String) - Method in class etomica.util.ScientificFormat
-
- setExpNegativeSuffix(String) - Method in class etomica.util.ScientificFormat
-
- setExponentialMode() - Method in class etomica.util.ScientificFormat
-
- setExpPositivePrefix(String) - Method in class etomica.util.ScientificFormat
-
- setExpPositiveSuffix(String) - Method in class etomica.util.ScientificFormat
-
- setExpPSpan(double) - Method in class etomica.normalmode.MeterDDP
-
- setExpPSpan(double) - Method in class etomica.normalmode.MeterDP
-
- setExternalField(Vector) - Method in class etomica.potential.P1ExternalField
-
- setExtraData(IDataSource) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
Sets a data source used to draw an extra set of "atoms".
- setExtraTargetClusters(ClusterAbstract[]) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setFactory(SimulationRunner) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- setFalseLabel(String) - Method in class etomica.action.ActionToggle
-
Specifies the button's label when the toggle is set to false.
- setFalseLabel(String) - Method in class etomica.graphics.DeviceToggleButton
-
Specifies the button's label when the toggle is set to false.
- setFalseLabel(String) - Method in class etomica.graphics.DeviceToggleRadioButtons
-
Specifies the button's label when the toggle is set to false.
- setFile(File) - Method in class etomica.action.PDBWriter
-
Sets the file to write to.
- setFile(File) - Method in class etomica.action.XYZWriter
-
Sets the file to write to.
- setFile(String) - Method in class etomica.data.AccumulatorAverageFixedOutputFile
-
- setFile(String) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- setFileName(String) - Method in class etomica.action.PDBWriter
-
Sets the file name to write to.
- setFileName(String) - Method in class etomica.action.WriteConfiguration
-
- setFileName(String) - Method in class etomica.action.WriteConfigurationBinary
-
- setFileName(String) - Method in class etomica.action.XYZWriter
-
Sets the file name to write to.
- setFileName(String) - Method in class etomica.data.DataLogger
-
Define the name of the output file.
- setFileName(String) - Method in class etomica.dimer.IntegratorDimerMin
-
Set's the filename of the output of this integrator.
- setFileName(String) - Method in class etomica.dimer.IntegratorDimerRT
-
Set's the filename of the output of this integrator.
- setFilename(String) - Method in class etomica.models.oneDHardRods.WriteHistograms
-
- setFileName(String) - Method in class etomica.normalmode.NormalModesMolecular
-
- setFileName(String) - Method in class etomica.normalmode.NormalModesPotential
-
- setFilename(String) - Method in class etomica.normalmode.WriteS
-
- setFileWriter(FileWriter) - Method in class etomica.data.DataArrayWriter
-
- setFileWriter(FileWriter) - Method in interface etomica.data.DataLogger.DataWriter
-
Sets the FileWriter to be used for actual file I/O.
- setFileWriter(FileWriter) - Method in class etomica.data.DataTableWriter
-
- setFilter(Predicate<IAtom>) - Method in class etomica.modules.droplet.MeterDeformation
-
- setFitToWindow(boolean) - Method in class etomica.graphics.DisplayTable
-
If true, columns will be squeezed so table fits to window; if false,
table will exceed window size, and to view full width must be placed in a
scroll pane.
- setFixedCOM(boolean) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- setFixedDaDef(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- setFixedDeltaU(double) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- setFixedDeltaU(double) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- setFixedDeltaU(double) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- setFixedDeltaU(double) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- setFixedOrientation(boolean) - Method in class etomica.virial.MCMoveChangeBondLength
-
- setFixedSpecies(ISpecies) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
- setFixedWall(FixedWall) - Method in class etomica.interfacial.IntegratorFixedWall
-
- setFlexCancelOnly(boolean) - Method in class etomica.virial.cluster.VirialDiagrams
-
This method only effects the graphs returned by getMSMCGraphs
- setFlexCancelOnly(boolean) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
This method only effects the graphs returned by getMSMCGraphs
- setFlexibleMode() - Method in class etomica.util.ScientificFormat
-
- setFluctuationFactor(double) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- setFluidNbrDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- setFont(JmolFont) - Method in class org.jmol.g3d.Graphics3D
-
- setFont(JmolFont) - Method in class org.jmol.util.GData
-
- setFontFid(byte) - Method in class org.jmol.g3d.Graphics3D
-
- setFontFid(byte) - Method in class org.jmol.util.GData
-
- setForce(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setForceconstant(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setForceconstant(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setForceSum(PotentialCalculationForceSum) - Method in class etomica.integrator.IntegratorVelocityVerlet
-
- setForceSum(PotentialCalculationForceSum) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- setFrac(double) - Method in class etomica.normalmode.MCMoveHarmonicEin
-
Sets the fraction of the systems energy from the normal mode
contribution.
- setFrac(double) - Method in class etomica.normalmode.MeterBoltzmannHarmonic
-
Sets the fraction that the system is coupled to measured energy.
- setFrac(double) - Method in class etomica.normalmode.MeterBoltzmannTarget
-
- setFrac(double) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- setFrac(double) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- setFrameProperties() - Method in class etomica.virial.GUI.containers.AppFrameMixtureBuilder
-
- setFreeRadicalColor(AtomType, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- setFrequency(MCMove, double) - Method in class etomica.integrator.mcmove.MCMoveManager
-
Sets the trial frequency for the given move to the given frequency.
- setFugacityFraction(double[]) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
Specifies the fugacity fractions for the set of species that can participate in
an exchange move.
- setFullBondColor(AtomType, Color) - Method in class etomica.modules.catalysis.ColorSchemeRadical
-
- setFullColor(AtomType, Color) - Method in class etomica.modules.chainequilibrium.ColorSchemeRadical
-
- setFunction(IFunction) - Method in class etomica.data.DataSourceFunction
-
- setFunction(FunctionInvertible) - Method in class etomica.modifier.ModifierFunctionWrapper
-
- setG(double) - Method in class etomica.modules.droplet.P1Smash
-
- setG1(Graph) - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- setG2(Graph) - Method in class etomica.graph.isomorphism.AbstractSearchState
-
- setGamma(double) - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- setGamma(double) - Method in class etomica.potential.P3BondAngleDreiding
-
Sets the characteristic energy of the potential
- setGammaPositionAndOrientation(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setGBplane(int[]) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
Allows a user to specify a plane for GB
- setGlobal() - Method in class org.jmol.script.ScriptVariable
-
- setGlobalMoveInterval(double) - Method in class etomica.integrator.IntegratorManagerMC
-
Sets the average interval between box-swap trials.
- setGoal(int) - Method in class etomica.graph.traversal.AbstractTraversal
-
- setGreyscaleMode(boolean) - Method in class org.jmol.util.GData
-
controls greyscale rendering
- setGroupingSize(int) - Method in class etomica.util.ScientificFormat
-
- setGroupingUsed(boolean) - Method in class etomica.util.ScientificFormat
-
- setH(double) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- setH(double) - Method in class etomica.math.numerical.FiniteDifferenceDerivative
-
- setH(double) - Method in class etomica.spin.P1MagneticField
-
- setHardCoreDiamterSq(double) - Method in class etomica.potential.P22CLJQ
-
- setHardCoreDiamterSq(double) - Method in class etomica.potential.P2LJQ
-
- setHardCoreDiamterSq(double) - Method in class etomica.rotation.P2LJDipole
-
- setHarmonicFudge(double) - Method in interface etomica.normalmode.NormalModes
-
Set the fudge factor applied to frequencies.
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModes1DHR
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModes2D
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModes3D
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesFromFile
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesMolecular
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesPotential
-
- setHarmonicFudge(double) - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- setHarmonicFudge(double) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setHarmonicPressure(double[], double) - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- setHarmonicWV(int[]) - Method in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- setHarmonicWV(int) - Method in class etomica.normalmode.MCMoveSingleMode
-
The harmonic wavevector and all wavevectors with higher numbers are not
able to be changed by this MCMove.
- setHashMapAtomsetIterator(HashMap<String[], AtomsetIteratorBasisDependent>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setHashMapAtomTypeLikePairs(HashMap<String[], AtomType[]>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setHashMapAtomTypesUnlikePairs(HashMap<String[], AtomType[]>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- setHashMapPotentialIntraBonded(HashMap<String[], IPotential>) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setHashMapPotentialNonBonded() - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- setHashMapPotentialNonBonded(HashMap<String[], IPotential>) - Method in class etomica.virial.GUI.components.HashMapPotentialNonBonded
-
- setHeight(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
In less than or equal to zero, the height is not
constrained on the output image.
- setHello(String) - Method in class etomica.server.EtomicaServerConfig
-
- setHexagonal(boolean) - Method in class etomica.modules.materialfracture.MeterElongation
-
- setHexagonal(boolean) - Method in class etomica.modules.materialfracture.MeterStrain
-
- setHexagonal(boolean) - Method in class etomica.modules.materialfracture.StrainColorScheme
-
- setHistogram(Histogram) - Method in class etomica.data.AccumulatorHistogram
-
- setHistogram(Histogram) - Method in class etomica.models.oneDHardRods.WriteHistograms
-
- setHistogramFactory(AccumulatorAverageBootstrap.HistogramFactory) - Method in class etomica.data.AccumulatorAverageBootstrap
-
- setHistogramming(boolean) - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- setHistogramSink(int, IDataSink) - Method in class etomica.data.AccumulatorAverageBootstrap
-
Sets the sink that will receive histograms for a block when pushHistograms is called.
- setHistory(History) - Method in class etomica.data.AccumulatorHistory
-
- setHistoryLength(int) - Method in interface etomica.data.history.History
-
Sets the number of data points to be tracked by the History.
- setHistoryLength(int) - Method in class etomica.data.history.HistoryCollapsing
-
Sets the number of values kept in the history.
- setHistoryLength(int) - Method in class etomica.data.history.HistoryComplete
-
Sets the number of values kept in the history.
- setHistoryLength(int) - Method in class etomica.data.history.HistoryScrolling
-
Sets the number of values kept in the history.
- setHOptimizer(boolean) - Method in class etomica.conjugategradient.FiniteDifferenceDerivativeCG
-
- setId(int) - Method in class etomica.virial.GUI.components.ArrayMoleculeDisplayList
-
- setID(int) - Method in class g3dsys.images.Figure
-
Set the ID of the figure.
- setIdentity() - Method in class org.jmol.util.Matrix3f
-
Sets this Matrix3f to identity.
- setIdentity() - Method in class org.jmol.util.Matrix4f
-
Sets this Matrix4f to identity.
- setIgnoredAtomType(AtomType) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
- setIgnoreOverlap(boolean) - Method in class etomica.action.IntegratorReset
-
- setIgnoreOverlap(boolean) - Method in class etomica.action.SimulationRestart
-
- setIgnoreOverlap(boolean) - Method in class etomica.zeolite.ZeoliteSimStart
-
- setIgnoreReferenceAvg(boolean) - Method in class etomica.virial.overlap.DataVirialOverlap
-
Directs this class to ignore the reference average when deciding how
much time to spend on each system.
- setImage(Image) - Method in class etomica.util.Grabber.ImagePanel
-
- setImageShells(int) - Method in class etomica.graphics.DisplayBox
-
Changes the value of image shells, and increases/decreases scale accordingly.
- setImax(int) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- setImportantAtoms() - Method in class etomica.action.IntegratorDimerApproach
-
- setIncludeACInError(boolean) - Method in class etomica.data.AccumulatorAverage
-
Include correction to the uncertainty from block correlation function as
prescribed in
Kolafa, Jiri(1986) 'Autocorrelations and subseries averages in Monte
Carlo Simulations', Molecular Physics (59) 1035
- setIncludeAdiabatic(boolean) - Method in class etomica.graphics.DeviceThermoSelector
-
- setIncludeHeader(boolean) - Method in class etomica.data.DataArrayWriter
-
Directs the writer to include column headers or not
- setIncludeHeader(boolean) - Method in class etomica.data.DataTableWriter
-
Directs the writer to include column headers or not
- setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterHyperVirial
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPotentialEnergy
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPressure
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPressureMolecular
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.data.meter.MeterPressureTensor
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.liquidLJ.MeterPU
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.modules.vle.MeterPressure2
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.normalmode.MeterPressureSuperBox
-
Sets flag indicating whether calculated energy should include
long-range correction for potential truncation (true) or not (false).
- setIncludeLrc(boolean) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- setIncludeLrc(boolean) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- setIncludeLrc(boolean) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- setIncludeLrc(boolean) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- setIncludeLrc(boolean) - Method in class etomica.potential.IteratorDirective
-
Sets flag indicating if lrc potentials (long-range correction) should be
included.
- setIndex(int) - Method in class etomica.atom.Atom
-
- setIndex(int) - Method in class etomica.atom.AtomType
-
Informs the IAtomType what its index should be.
- setIndex(int) - Method in interface etomica.atom.IAtom
-
Informs the IAtom of its index within the atoms of its parent molecule.
- setIndex(int) - Method in class etomica.box.Box
-
Informs the Box what its index is.
- setIndex(int) - Method in interface etomica.molecule.IMolecule
-
Informs the IMolecule of its index.
- setIndex(int) - Method in class etomica.molecule.Molecule
-
- setIndex(int) - Method in interface etomica.species.ISpecies
-
Informs the ISpecies what its index should be.
- setIndex(int) - Method in class etomica.species.Species
-
- setIndexed(int) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Tells the PNG encoder to reduce the image to 256 colors, so the
PNG file is indexed.
- setIndexSelectedSpecies(int) - Method in exception etomica.virial.GUI.components.ExceptionDoNotRemoveSpecies
-
- setInflateDimensions(boolean[]) - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
For anisotropic volume change, indicates dimension in which volume is perturbed.
- setInflater(BoxInflate) - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- setInflater(BoxInflate) - Method in class etomica.normalmode.MCMoveVolumeMonoclinic
-
- setInflater(BoxInflate) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- setInflater(BoxInflate) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- setInitialStateConditions(double, double) - Method in class etomica.kmc.IntegratorKMC
-
- setInitialStateConditions(double, double) - Method in class etomica.kmc.IntegratorKMCCluster
-
- setInitVolume(Vector) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
-
- setInitVolume(Vector) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- setInnerIterator(GraphIterator) - Method in class etomica.graph.iterators.CartesianIterator
-
- setInnerList(IAtomList) - Method in class etomica.atom.iterator.ApiInterArrayList
-
Sets the list that will be used to generate the pairs.
- setInnerList(IMoleculeList) - Method in class etomica.molecule.iterator.MpiInterArrayList
-
Sets the list that will be used to generate the pairs.
- setInnerPermutator(DefaultPermutator) - Method in class etomica.graph.iterators.CartesianPermutator
-
- setInnerWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
- setInnerWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
- setInputData(double[], double[]) - Method in class etomica.math.numerical.AkimaSpline
-
- setInputData(double[], double[], double[]) - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- setInputData(double[], double[], double[]) - Method in class etomica.math.numerical.AkimaSplineSmootherDy
-
- setInputData(double[], double[], double[], double[]) - Method in class etomica.math.numerical.AkimaSplineSmootherDy
-
Set the nominal values for x and y and uncertainty in y (ey).
- setInputFileName(String) - Method in class etomica.util.ReadParameters
-
Sets the fileName to read the parameters from.
- setInputFileName(String) - Method in class etomica.util.WriteParameters
-
Sets the fileName to read the parameters from.
- setInt(int) - Method in class org.jmol.util.Rgb16
-
- setInteger(boolean) - Method in class etomica.graphics.DeviceBox
-
Sets a flag indicating if the value should be displayed as an integer.
- setIntegerDisplay(boolean) - Method in class etomica.graphics.DisplayTextBox
-
- setIntegrationParameters(double, double, double, double, int, int) - Method in class etomica.models.oneDHardRods.DoubleIntegralEtas
-
- setIntegrator(Integrator) - Method in interface etomica.action.IntegratorAction
-
- setIntegrator(Integrator) - Method in class etomica.action.IntegratorActionAdapter
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.DataProcessorChemicalPotential
-
- setIntegrator(IntegratorHard) - Method in class etomica.data.DataSourceCountCollisions
-
- setIntegrator(Integrator) - Method in class etomica.data.DataSourceCountSteps
-
- setIntegrator(IntegratorMD) - Method in class etomica.data.DataSourceCountTime
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
-
Sets the integrator.
- setIntegrator(IntegratorHard) - Method in class etomica.data.DataSourceTensorVirialHard
-
Informs meter of the integrator for its box, and zeros elapsed-time counter
- setIntegrator(IntegratorMD) - Method in class etomica.data.meter.MeterKineticEnergyFromIntegrator
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPotentialEnergyFromIntegrator
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPressure
-
Sets the integrator associated with this instance.
- setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
Sets the integrator associated with this instance.
- setIntegrator(IntegratorHard) - Method in class etomica.data.meter.MeterPressureHard
-
Registers meter as a collisionListener to the integrator, and sets up
a DataSourceTimer to keep track of elapsed time of integrator.
- setIntegrator(IntegratorHard) - Method in class etomica.data.meter.MeterPressureHardTensor
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterPressureMolecular
-
Sets the integrator associated with this instance.
- setIntegrator(IntegratorVelocityVerlet) - Method in class etomica.data.meter.MeterPressureTensorFromIntegrator
-
- setIntegrator(IntegratorBox) - Method in class etomica.data.meter.MeterWidomInsertion
-
Sets the integrator associated with this class.
- setIntegrator(IntegratorBox) - Method in class etomica.graphics.DeviceThermoSelector
-
- setIntegrator(IntegratorBox) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Sets the integrator associated with this class.
- setIntegrator(IntegratorVelocityVerlet) - Method in class etomica.meam.DataProcessorCvMD
-
- setIntegrator(IntegratorHard) - Method in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
Registers meter as a collisionListener to the integrator, and sets up
a DataSourceTimer to keep track of elapsed time of integrator.
- setIntegrator(IntegratorHard) - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- setIntegrator(IntegratorHard) - Method in class etomica.modules.mu.DataSourceWallPressureMu
-
Registers meter as a collisionListener to the integrator, and sets up
a DataSourceTimer to keep track of elapsed time of integrator.
- setIntegrator(IntegratorPolymer) - Method in class etomica.modules.rheology.MeterNormalStress
-
- setIntegrator(IntegratorPolymer) - Method in class etomica.modules.rheology.MeterViscosity
-
- setIntegrator(IntegratorBox) - Method in class etomica.modules.rosmosis.MeterFlux
-
- setIntegrator(IntegratorHarmonic) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Sets the integrator for the device.
- setIntegrator(IntegratorHarmonic) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Sets the integrator for the device.
- setIntegrator(IntegratorBox) - Method in class etomica.normalmode.MeterPressureSuperBox
-
Sets the integrator associated with this instance.
- setIntegrator(IntegratorBox) - Method in class etomica.potential.PotentialCalculationPressureTensor
-
Sets an integrator to use a source for the temperature to compute the
kinetic portion of the pressure.
- setIntegrator(Integrator) - Method in class etomica.zeolite.MSDCoordWriter
-
- setIntegratorMC(IntegratorMC, int) - Method in class etomica.integrator.IntegratorMD
-
A Monte Carlo integrator is employed with this MD integrator when performing hybrid MD/MC
sampling.
- setIntegratorOverlap(IntegratorOverlap) - Method in class etomica.normalmode.SimOverlapModule
-
- setIntegrators(IntegratorMC, IntegratorMD, IRandom) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setIntegrators(IntegratorBox, IntegratorBox, IntegratorManagerMC) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Sets the integrator for the device.
- setInteractionRange(double) - Method in class etomica.nbr.CriterionPositionWall
-
Informs the criterion of the interaction range of the wall potential.
- setInteractionRange(double) - Method in class etomica.nbr.CriterionSimple
-
- setInteractionRange(double) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- setIntercepts(double, double, double) - Method in class etomica.math.geometry.Plane
-
Reorients and positions the plane so that its intercepts with the
x-, y-, and z-axes are the given values, respectively.
- setInteriorColor(Color) - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
-
- setInterval(long) - Method in class etomica.data.DataPumpListener
-
- setInterval(int) - Method in class etomica.integrator.IntegratorListenerAction
-
- setInterval(int) - Method in class etomica.integrator.IntegratorListenerGroupSeries
-
- setIntraMolecular(boolean) - Method in class etomica.nbr.CriterionMolecular
-
Configures to accept intra- (if argument is true) or inter-
(if argument is false) molecular pairs.
- setIntraMolecularCriterion(NeighborCriterion) - Method in class etomica.nbr.CriterionInterMolecular
-
Configures to use the given criterion for intramolecular pairs.
- setInverseNormixes() - Static method in class org.jmol.util.Normix
-
- setIs256() - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- setIs864() - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- setIsAlpha() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsAlpha() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setIsAppend(boolean) - Method in class etomica.action.XYZWriter
-
- setIsBeta() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsBetaHCP() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsBetaLatticeSum() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsDoLatticeSum() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheres
-
- setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheresCustom
-
- setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheresHetero
-
- setIsDynamic(boolean) - Method in class etomica.species.SpeciesSpheresMono
-
- setIsFluctuationFromAvg(boolean) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- setIsGamma() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setIsGamma() - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setIsInteracting(boolean, int) - Method in class etomica.nbr.list.AtomPotentialList
-
Sets whether the atom is interacting or not with the potential corresponding to the given index.
- setIsInteracting(boolean, int) - Method in class etomica.nbr.list.molecule.MoleculePotentialList
-
Sets whether the molecule is interacting or not with the potential
corresponding to the given index.
- setIsothermal() - Method in class etomica.graphics.DeviceThermoSlider
-
Set the Isothermal button to its selected state.
- setIsothermal(boolean) - Method in class etomica.integrator.IntegratorBox
-
- setIsothermal(boolean) - Method in class etomica.integrator.IntegratorMD
-
- setIsothermal(boolean) - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setIsothermal(boolean) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setIsothermal() - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the Isothermal button to its selected state.
- setIsothermalButtonsVisibility(boolean) - Method in class etomica.graphics.DeviceThermoSlider
-
- setIsothermalButtonsVisibility(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
- setIsUpperBound(boolean) - Method in class etomica.modules.multiharmonic.DataProcessorBounds
-
- setIterator(AtomIterator) - Method in class etomica.data.DataSourceRmsVelocity
-
Sets the iterator defining the atoms for which the RMS velocity is
calculated.
- setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterKineticEnergy
-
Sets the iterator that defines the atoms which are summed for
their total kinetic energy.
- setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterLocalDensity
-
- setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterLocalMoleFraction
-
- setIterator(AtomIteratorBoxDependent) - Method in class etomica.data.meter.MeterMeanSquareDisplacement
-
- setIterator(MoleculeIteratorAllMolecules) - Method in class etomica.data.meter.MeterRadiusGyration
-
Mutator method for the iterator that generates the atom pairs used to
tabulate the ROG.
- setIterator(AtomIteratorBoxDependent) - Method in class etomica.zeolite.MSDCoordWriter
-
- setJmax(int) - Method in class etomica.conjugategradient.NonLinearConjugateGradients
-
- setJSpinnerCountOfSpecies1(JSpinner, int) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setK(Vector) - Method in class etomica.lattice.LatticeSum
-
- setK(Vector) - Method in class etomica.lattice.LatticeSumCrystal
-
- setK(Vector) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- setK(Vector) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
- setKappa(double) - Method in class etomica.yukawa.P2Yukawa
-
Mutator methods for size and energy parameters.
- setKinetic(DataSourceScalar) - Method in class etomica.data.meter.MeterEnergy
-
- setKineticEnergyMeter(DataSourceScalar) - Method in class etomica.data.meter.MeterTemperature
-
- setLabel(String) - Method in class etomica.data.DataInfoFactory
-
Sets the label
- setLabel(String) - Method in interface etomica.data.IDataInfoFactory
-
Sets the label
- setLabel(String) - Method in class etomica.graphics.DeviceBox
-
Sets the value of a descriptive label using the given string.
- setLabel(String) - Method in class etomica.graphics.DeviceButton
-
Sets the value of a descriptive label using the given string.
- setLabel(String) - Method in class etomica.graphics.DeviceButtonGroup
-
Sets the label for the group of radio buttons
- setLabel(String) - Method in class etomica.graphics.DeviceSelector
-
- setLabel(String) - Method in class etomica.graphics.DeviceSlider
-
Sets the value of a descriptive label using the given string.
- setLabel(String) - Method in class etomica.graphics.DeviceSpinner
-
Sets the value of a descriptive label using the given string.
- setLabel(String) - Method in class etomica.graphics.Display
-
Accessor method of the label describing the display.
- setLabel(String) - Method in class etomica.graphics.DisplayTextBox
-
Sets the value of a descriptive label using the given string.
- setLabel(String) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- setLabel(String) - Method in class etomica.modifier.ModifierGeneral
-
- setLabel(String) - Method in class etomica.zeolite.DeviceButtonSingle
-
Sets the value of a descriptive label using the given string.
- setLabelPosition(Constants.CompassDirection) - Method in class etomica.graphics.DeviceBox
-
- setLabelPosition(Constants.CompassDirection) - Method in class etomica.graphics.DisplayTextBox
-
- setLabelPosition(Constants.CompassDirection) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- setLabelType(DeviceBox.LabelType) - Method in class etomica.graphics.DeviceBox
-
Sets the label type to "border" or "string".
- setLabelType(DisplayTextBox.LabelType) - Method in class etomica.graphics.DisplayTextBox
-
- setLabelType(DisplayTextBox.LabelType) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- setLambda(double) - Method in class etomica.modules.adsorption.EOSSW
-
- setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- setLambda(double) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- setLambda(double) - Method in class etomica.potential.P2DoubleWell
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.potential.P2PenetrableSquareWell
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.potential.P2SquareWell
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.potential.P2SquareWellRobust
-
Accessor method for well-diameter multiplier.
- setLambda(double) - Method in class etomica.potential.P2TriangleWell
-
- setLanguage(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the user language.
- setLattice(Vector[], Vector[]) - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- setLattice(FiniteLattice) - Method in class etomica.graphics.ColorSchemeCell
-
- setLattice(FiniteLattice) - Method in class etomica.lattice.CellLattice.NeighborIterator
-
- setLattice(SpaceLattice) - Method in class etomica.lattice.LatticeSum
-
- setLattice(FiniteLattice) - Method in class etomica.lattice.RectangularLattice.Iterator
-
- setLattice(FiniteLattice) - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Sets the lattice from which the iterates are given.
- setLattice(FiniteLattice) - Method in class etomica.lattice.RectangularLatticeNbrIteratorSquare
-
- setLattice(FiniteLattice) - Method in interface etomica.lattice.SiteIterator
-
Sets the lattice having the sites to be given by this iterator.
- setLattice(CellLattice) - Method in class etomica.nbr.cell.ApiAACell
-
- setLattice(CellLattice) - Method in class etomica.nbr.cell.molecule.MpiAACell
-
- setLatticeBox(Box) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- setLatticeBox(Box) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- setLatticeConstant(double) - Method in interface etomica.lattice.CubicLattice
-
Sets the size of the unit cell, the length of each edge.
- setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicBcc
-
The lattice constant is the size of the cubic primitive vectors
of the lattice underlying this crystal.
- setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicDiamond
-
The lattice constant is the size of the cubic primitive vectors
of the lattice underlying this crystal.
- setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicFcc
-
The lattice constant is the size of the cubic primitive vectors
of the lattice underlying this crystal.
- setLatticeConstant(double) - Method in class etomica.lattice.LatticeCubicSimple
-
The lattice constant is the size of the cubic primitive vectors.
- setLatticeCorrec(double) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- setLatticeEnergy(double) - Method in class etomica.models.nitrogen.MeterRotPerturbMolecule
-
- setLatticeEnergy(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setLatticeEnergy(double) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterBoltzmannHarmonic
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterBoltzmannTarget
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterDADB
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterDirectSamplingTarget
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterTargetTP
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkBennetHarmonic
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkBennetTarget
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetBennet
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.MeterWorkTargetUmbrella
-
- setLatticeEnergy(double) - Method in class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
-
- setLayers(int) - Method in class g3dsys.images.ImageShell
-
Sets the number of image shell layers to use
- setLeafIndex(int) - Method in class etomica.atom.Atom
-
- setLeafIndex(int) - Method in interface etomica.atom.IAtom
-
Sets the atom's global index to the give value.
- setLegend(DataTag[], String) - Method in class etomica.graphics.DisplayPlot
-
- setLength(double) - Method in class etomica.math.geometry.LineSegment
-
Sets the length of the segment to the given value, keeping
its orientation and the position of its midpoint fixed.
- setLength(double) - Method in class etomica.models.hexane.CheckCBMCHexane
-
- setLength(double) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
-
- setLength(int) - Method in class etomica.modules.statistics.DataCollector
-
- setLength(int) - Method in class org.jmol.util.StringXBuilder
-
- setLengthAlkaneChain(int, int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setLinPSpan(double) - Method in class etomica.normalmode.MeterDDP
-
- setLinPSpan(double) - Method in class etomica.normalmode.MeterDP
-
- setLiquidColor(Color) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- setLiquidFilter(AtomFilter) - Method in class etomica.modules.droplet.P2Cohesion
-
- setList(IAtomList) - Method in class etomica.atom.iterator.ApiIntraArrayList
-
Sets the list that will be used to generate the pairs.
- setList(IAtomList) - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Sets the list for iteration.
- setList(IMoleculeList) - Method in class etomica.molecule.iterator.MoleculeIteratorArrayListSimple
-
Sets the list for iteration.
- setList(IMoleculeList) - Method in class etomica.molecule.iterator.MpiIntraArrayList
-
Sets the list that will be used to generate the pairs.
- setLnBias(int, double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- setLnBias(int, double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- setLocale(Locale) - Static method in class etomica.graph.view.rasterizer.Messages
-
Implements Localizable.setLocale(Locale).
- setLocalVisitor(TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal
-
- setLogger(LoggerInterface) - Static method in class org.jmol.util.Logger
-
Replaces the current logger implementation by a new one.
- setLogLevel(int) - Static method in class org.jmol.util.Logger
-
Activates all logging levels up through a given level.
- setLongWall(int, boolean, boolean) - Method in class etomica.potential.P1HardBoundary
-
- setLowerTorsLimit(double) - Method in class etomica.models.hexane.CheckCBMCHexane
-
- setM(Matrix3f) - Method in class org.jmol.util.AxisAngle4f
-
Sets the value of this axis-angle to the rotational component of the passed
matrix.
- setM(Matrix3f) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to the double value of the Matrix3f argument.
- setM(Matrix4f) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to a copy of the passed matrix m1.
- setM(Matrix3f) - Method in class org.jmol.util.Quaternion
-
- setM3(Matrix3f) - Method in class org.jmol.util.Matrix4f
-
Sets the rotational component (upper 3x3) of this matrix to the matrix
values in the single precision Matrix3f argument; the other elements of
this matrix are initialized as if this were an identity matrix (ie, affine
matrix with no translational component).
- setMacrostateManager(MacrostateManager) - Method in class etomica.tmmc.IntegratorTMMC
-
- setMakeLrc(boolean) - Method in class etomica.potential.P2SoftSphericalTruncated
-
- setMakeReeHover(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to generate Ree-Hoover diagrams.
- setMass(double) - Method in class etomica.chem.elements.ElementSimple
-
Sets mass of this element and updates reciprocal mass accordingly.
- setMass(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setMass(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
Sets the mass; we assume the reduced mass is m/2 (correct for particles
with identical mass).
- setMass(double) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
-
Sets the mass; we assume the reduced mass is m/2 (correct for particles
with identical mass).
- setMass(double) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
-
- setMass(double) - Method in class etomica.units.systems.LJ
-
- setMax(int) - Method in class etomica.lattice.IndexIteratorIncreasing
-
Sets a new maximum for iteration.
- setMaxAdjustInterval(long) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
The step size is adjusted every adjustInterval trials.
- setMaxBlocks(int) - Method in class etomica.data.AccumulatorAverageCollapsing
-
Changes the maximum number of blocks.
- setMaxBonds(int) - Method in class etomica.association.AssociationHelperBranched
-
- setMaxBonds(int) - Method in class etomica.association.AssociationHelperMolecule
-
- setmaxCosPhi(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- setmaxCosPhi(double) - Method in class etomica.association.BiasVolumeAceticAcid
-
- setmaxCosTheta(double) - Method in class etomica.association.BiasVolume2SiteAceticAcid
-
- setmaxCosTheta(double) - Method in class etomica.association.BiasVolumeAceticAcid
-
- setMaxDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- setMaxDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- setMaxElement(int) - Method in class etomica.lattice.IndexIteratorTriangular
-
Sets the largest allow value for any element to have.
- setMaxElement(int) - Method in class etomica.lattice.LatticeSum
-
Specifies the largest index element that will be included in the lattice sum.
- setMaxElementMin(int) - Method in class etomica.lattice.IndexIteratorTriangular
-
- setMaxHeight(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
If less than or equal to zero, the maximum height
does not have any effect on the output image.
- setMaximum(double) - Method in class etomica.graphics.DeviceSlider
-
Sets maximum value of slider; should be called after
any calls to setPrecision.
- setMaximum(double) - Method in class etomica.graphics.DeviceSpinner
-
Sets maximum value of slider
- setMaximum(double) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the maximum value for the temperature.
- setMaximum(double) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the maximum value for the temperature.
- setMaximum(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the maximum value for the N-Cell #.
- setMaximum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the maximum value for the x- and y-Cell #.
- setMaximum(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the maximum value for the eigenvalue #.
- setMaximum(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the maximum value for the wavevector #.
- setMaximumFractionDigits(int) - Method in class etomica.util.ScientificFormat
-
- setMaximumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
-
- setMaximumSeparation(double) - Method in class etomica.potential.P2Fene
-
Accessor method for harmonic energy parameter
- setMaxIndex(int) - Method in class etomica.veos.HardRods
-
- setMaxIndex(int) - Method in class etomica.veos.VanderWaals
-
- setMaxInsertDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- setMaxInsertDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- setMaxIterations(int) - Method in class etomica.integrator.IntegratorRigidIterative
-
- setMaxIterations(int) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- setMaxIterations(int) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- setMaxIterations(int) - Method in class etomica.modules.interfacial.FitTanh
-
- setMaxIterations(int) - Method in class etomica.surfacetension.FitTanh
-
- setMaxLatticeShell(int) - Method in class etomica.lattice.LatticeSumCrystal
-
Specifies the largest index element that will be included in the lattice sum.
- setMaxLatticeShell(int) - Method in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
Specifies the largest index element that will be included in the lattice sum.
- setMaxLatticeShell(int) - Method in class etomica.normalmode.HarmonicCrystal
-
- setMaxLatticeShell(int) - Method in class etomica.normalmode.HarmonicCrystalSsFccNxy
-
- setMaxLatticeShell(int) - Method in class etomica.normalmode.NormalModesPotential
-
- setMaxLatticeShell(int) - Method in class etomica.paracetamol.HarmonicCrystalMonoclinic
-
- setMaxLatticeShell(int) - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic
-
- setMaxLatticeShell(int) - Method in class etomica.paracetamol.LatticeSumCrystalParacetamol
-
Specifies the largest index element that will be included in the lattice sum.
- setMaxLatticeShell(int) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setMaxLength(int) - Method in class etomica.association.MCMoveAtomMonomer
-
- setMaxLength(int) - Method in class etomica.association.MCMoveAtomSmer
-
- setMaxLength(int) - Method in class etomica.association.MCMoveBiasUB
-
- setMaxLength(int) - Method in class etomica.association.MCMoveRotateAssociated
-
- setMaxNbrsVapor(int) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- setMaxNumBlocks(int) - Method in class etomica.data.AccumulatorAverageBootstrap
-
Sets the maximum number of blocks of raw data to be 1<
- setMaxPhi(double) - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- setMaxPhi(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- setMaxSample(double) - Method in class etomica.data.AccumulatorAverageCollapsingLogAB
-
- setMaxSleep(int) - Method in class etomica.graphics.DeviceDelaySlider
-
- setMaxSteps(long) - Method in class etomica.action.ActionIntegrate
-
Mutator method for the number of doStep steps to be
performed by this integrator after it is started.
- setMaxSteps(long) - Method in class etomica.action.activity.ActivityIntegrate
-
Mutator method for the number of doStep steps to be
performed by this integrator after it is started.
- setMaxWidth(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
If less than or equal to zero, the maximum width
does not have any effect on the output image.
- setMaxWidth(int) - Method in class etomica.util.ScientificFormat
-
the the maximum width of the decimal format.
- setMCMove(MCMoveStepDependent) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
- setMCMoveClusterTorsionMulti(MCMoveClusterTorsionMulti[]) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setMCMoveInsertDelete(MyMCMove, MyMCMove) - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setMCMoves(MCMove[]) - Method in class etomica.integrator.mcmove.MCMoveManager
-
Sets moves in given array to be integrator's set of moves, deleting any
existing moves.
- setMDStepRepetitions(int) - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setMDStepRepetitions(int) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setMediaType(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the mediaType value.
- setMembraneDim(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setMembraneDim(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setMembraneThickness(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setMembraneThicknessPerLayer(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setMembraneWidth(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setMembraneWidth(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setMeter(DataSourceScalar) - Method in class etomica.graphics.DisplayScrollingGraph
-
Specifies the meter that generates the displayed value.
- setMeter(MeterNormalMode) - Method in class etomica.normalmode.WriteS
-
- setMeter(IDataSource) - Method in class etomica.virial.simulations.SimulationVirial
-
- setMeter(MeterVirial, int) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- setMeter(MeterVirial, int) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- setMeterPotentialEnergy(DataSourceScalar) - Method in class etomica.integrator.IntegratorBox
-
- setMeterTemperature(MeterTemperature) - Method in class etomica.integrator.IntegratorMD
-
Sets the temperature meter used to calculate temperature for
velocity rescaling.
- setMethanolParams(int) - Static method in class etomica.models.rowley.MethanolRouteParams
-
- setMillerIndex(int, int) - Method in class etomica.lattice.LatticePlane
-
Sets the i-th Miller index to h, keeping the others fixed.
- setMillerIndices(int[]) - Method in class etomica.lattice.LatticePlane
-
Sets the plane to the orientation specified by the given Miller indices
applied to the current primitive.
- setMinAdjustStep(double) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
When the step size is adjusted, it is adjusted by adjustStep.
- setMinBondedAtomDistance(double) - Method in class etomica.association.AssociationHelperBranched
-
- setMinBondedAtomDistance(double) - Method in class etomica.association.AssociationHelperDouble
-
- setMinBondedMoleculeDistance(double) - Method in class etomica.association.AssociationHelperMolecule
-
- setMinDistance(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- setMinimum(double) - Method in class etomica.graphics.DeviceSlider
-
Sets minimum value of slider; should be called after
any calls to setPrecision.
- setMinimum(double) - Method in class etomica.graphics.DeviceSpinner
-
Sets minimum value of spinner
- setMinimum(double) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the minimum value for the temperature.
- setMinimum(double) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the minimum value for the temperature.
- setMinimum(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the minimum value for the N-Cell #.
- setMinimum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the minimum value for the x- and y-Cell #.
- setMinimum(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the minimum value for the eigenvalue #.
- setMinimum(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the minimum value for the wavevector #.
- setMinimumFractionDigits(int) - Method in class etomica.util.ScientificFormat
-
- setMinimumIntegerDigits(int) - Method in class etomica.util.ScientificFormat
-
- setMinMax(int, int) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- setMinRadicalSites(int) - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
- setMobileSpecies(ISpecies) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
- setModelSelectedSpecies(ModelSelectedSpecies) - Method in class etomica.virial.GUI.models.AppModelMixtureBuilder
-
- setModelSpeciesSelection(ModelSpeciesSelection) - Method in class etomica.virial.GUI.models.AppModelMixtureBuilder
-
- setModeNum(int[]) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setModes(int[]) - Method in class etomica.normalmode.MCMoveHarmonicStep
-
Sets the indices of the harmonic modes of the k=0 wave vector which
should be sampled.
- setModifier(ModifierBoolean) - Method in class etomica.action.ActionToggle
-
Specifies the boolean modifier that is set between true and false by the
action.
- setModifier(Modifier) - Method in class etomica.graphics.DeviceBox
-
Specifies the modifier that receives the edit.
- setModifier(ModifierBoolean) - Method in class etomica.graphics.DeviceCheckBox
-
Returns the boolean modifier set by this button.
- setModifier(Modifier) - Method in class etomica.graphics.DeviceNSelector
-
- setModifier(Modifier) - Method in class etomica.graphics.DeviceSlider
-
- setModifier(Modifier) - Method in class etomica.graphics.DeviceSpinner
-
- setModifier(Modifier) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the temperature modifier object.
- setModifier(ModifierBoolean, String, String) - Method in class etomica.graphics.DeviceToggleButton
-
- setModifier(ModifierBoolean) - Method in class etomica.graphics.DeviceToggleRadioButtons
-
Returns the boolean modifier set by this button.
- setModifier(Modifier) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the temperature modifier object.
- setModifier(Modifier) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the eigenvalue # modifier object.
- setModifier(Modifier) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the wavevector # modifier object.
- setMolecule(IMolecule, IMolecule) - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
- setMolecule(IMolecule) - Method in class etomica.molecule.iterator.MoleculeIteratorArrayList
-
Sets the first atom for iteration.
- setMolecule(IMolecule) - Method in interface etomica.molecule.iterator.MoleculeIteratorMoleculeDependent
-
- setMolecule(IMolecule) - Method in class etomica.molecule.iterator.MoleculeIteratorSinglet
-
Defines atom returned by iterator and leaves iterator unset.
- setMolecule(int, int) - Method in class etomica.paracetamol.HarmonicCrystalOrthorhombic.LatticeEnergy
-
- setMolecule(int, int) - Method in interface etomica.paracetamol.LatticeEnergyParacetamol
-
- setMolecule(int, int) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol.Lattice2ndDerivative
-
- setMoleculeAgentManager(MoleculeAgentManager) - Method in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
- setMoleculeAgentManager(MoleculeAgentManager) - Method in class etomica.potential.PotentialCalculationTorqueSum
-
- setMoleculeInfo(ISpecies, P2SemiclassicalMolecular.MoleculeInfo) - Method in class etomica.potential.P2SemiclassicalMolecular
-
- setMoleculeListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setMoleculeListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setMoleculeListDisplayString(ArrayList<String>) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setMoleculeListDisplayTable(JTable) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setMoleculeListDisplayTable(JTable) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setMoleculeListDisplayTM(ModelMoleculeListDisplayTable_new) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setMoleculeListDisplayTM(ModelMoleculeListDisplayTable_new) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setMoleculeListDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setMoleculeLists(IMoleculeList[]) - Method in class etomica.box.AtomSetAllMolecules
-
Configures this list based on the given array of lists.
- setMoleculeOffset(Vector) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setMoleculeOffset(Vector) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setMoleculePosition(IMoleculePositionDefinition) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- setMolecules() - Method in class etomica.action.IntegratorDimerApproach
-
- setMoleculeSource(MoleculeSource) - Method in class etomica.integrator.mcmove.MCMoveMolecule
-
- setMoleculeSource(MoleculeSource) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
Sets the AtomSource this class uses to pick molecules to delete.
- setMoleculeSource(MoleculeSource) - Method in class etomica.models.hexane.MCMoveCBMC
-
Sets the AtomSource used to select molecules acted on by MC trials.
- setMoleculeSource(MoleculeSource) - Method in class etomica.virial.MCMoveClusterAngleBend
-
- setMoleculeSource(MoleculeSource) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- setMoment(double) - Method in class etomica.modules.vle.VLESim
-
- setMoment(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setMoment(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setMoment(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setMomentOfInertia(Vector) - Method in class etomica.species.SpeciesSpheresRotatingMolecule
-
Sets the species' moment of inertia to the given moment.
- setMomentSquare(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setMonomerColor(Color) - Method in class etomica.association.ColorSchemeSmer
-
Sets the color used for all dimers.
- setMonomerMonomerBondManager(AtomLeafAgentManager) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setMovable(boolean) - Method in class etomica.graphics.DisplayCanvas
-
- setMovable(boolean) - Method in class etomica.graphics.DisplayPolytope
-
- setMovableAtoms(double, Vector) - Method in class etomica.dimer.SimDimerLJadatom
-
- setMovableAtoms(double, Vector) - Method in class etomica.dimer.SimDimerMEAMadatom
-
- setMovableAtoms(double, Vector) - Method in class etomica.kmc.SimKMCLJadatom
-
- setMovableAtoms(double, Vector) - Method in class etomica.kmc.SimKMCMEAMadatom
-
- setMovableAtomsCube(Vector, Vector) - Method in class etomica.dimer.SimDimerMEAMGB
-
- setMovableAtomsList() - Method in class etomica.dimer.SimDimerMEAMGB
-
- setMovableAtomsSphere(double, Vector) - Method in class etomica.dimer.SimDimerMEAMGB
-
- setMove(MCMove) - Method in class etomica.data.DataSourceAcceptanceRatio
-
Sets the move for which the acceptance ratio is reported.
- setMoveManager(MCMoveManager) - Method in class etomica.integrator.IntegratorManagerMC
-
- setMoveManager(MCMoveManager) - Method in class etomica.integrator.IntegratorMC
-
- setMu(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
Sets a nominal bias for states that have not yet been visited.
- setMu(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
Mutator method for the chemical potential of the insertion/deletion species.
- setMu(double) - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteBiased
-
- setMu(double, double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setMu(double) - Method in class etomica.normalmode.DataSourceAvgPressure
-
- setMu(double) - Method in class etomica.normalmode.DataSourceFEHistogram
-
- setMu(double) - Method in class etomica.normalmode.DataSourceImposedFEFit
-
- setMu(double) - Method in class etomica.normalmode.DataSourceImposedFEHistogram
-
- setMu(double) - Method in class etomica.normalmode.DataSourcePMu
-
- setMV(Matrix3f, Vector3f) - Method in class org.jmol.util.Matrix4f
-
Initializes a Matrix4f from the rotation matrix
and translation.
- setN(int) - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- setN(int) - Method in class etomica.potential.P4TorsionDreiding
-
- setN(int) - Method in class etomica.veos.Ushcats
-
- setName(String) - Method in class etomica.data.meter.MeterDihedralAngle
-
- setName(String) - Method in class etomica.data.meter.MeterMomentumCOM
-
- setName(String) - Method in class etomica.data.meter.MeterPositionCOM
-
- setName(String) - Method in class etomica.data.meter.MeterPressureHardTensor
-
- setName(String) - Method in class etomica.data.meter.MeterRDF
-
- setName(String) - Method in class etomica.data.meter.MeterRDFPC
-
- setName(String) - Method in class etomica.data.meter.MeterTensorVelocity
-
- setName(String) - Method in class etomica.mappedRdf.MeterMappedRdf
-
- setName(String) - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- setName(String) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- setName(String) - Method in class etomica.normalmode.MeterNormalMode
-
- setName(String) - Method in class org.jmol.script.ScriptVariable
-
- setNBins(int) - Method in class etomica.data.AccumulatorHistogram
-
Sets the number of bins in each histogram.
- setNBins(int) - Method in interface etomica.data.histogram.Histogram
-
Sets the number of bins used by the Histogram.
- setNBins(int) - Method in class etomica.data.histogram.HistogramDiscrete
-
- setNBins(int) - Method in class etomica.data.histogram.HistogramExpanding
-
Sets the number of bins to n.
- setNBins(int) - Method in class etomica.data.histogram.HistogramNotSoSimple
-
- setNBins(int) - Method in class etomica.data.histogram.HistogramReweightedData
-
- setNBins(int) - Method in class etomica.data.histogram.HistogramSimple
-
- setNbrDistance(double) - Method in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- setNCellModifier(Modifier) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the n-Cell # modifier object.
- setNCellNum(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the current value for the N-Cell # slider/text box.
- setNCellNum(int) - Method in class etomica.normalmode.NormalModes3D
-
- setNCells(int[]) - Method in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- setNCells(int[]) - Method in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- setNCellsX(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setNCellsX(int) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setNCellsZ(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setNCellsZ(int) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setNCrossLinkersAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- setNDiAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- setNDiol(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- setNegativePrefix(String) - Method in class etomica.util.ScientificFormat
-
- setNegativeSuffix(String) - Method in class etomica.util.ScientificFormat
-
- setNeighborDistance(double) - Method in class etomica.lattice.CellLattice.NeighborIterator
-
Defines neighbors to be all cells that are within the given distance
from a central cell.
- setNeighborRange(double) - Method in class etomica.nbr.CriterionPositionWall
-
Sets the neighbor range of the criterion.
- setNeighborRange(double) - Method in class etomica.nbr.CriterionSimple
-
- setNeighborRange(double) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- setNewWindowParametersForExport() - Method in class org.jmol.util.GData
-
- setNGraft(int) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setNInsert(int) - Method in class etomica.data.meter.MeterWidomInsertion
-
Number of Widom insertions attempted with each call to currentValue
- setNInsert(int) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
Number of Widom insertions attempted with each call to currentValue
- setNInsert(int) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Number of Widom insertions attempted with each call to currentValue
- setNMajor(int) - Method in class etomica.graphics.DeviceSlider
-
- setNMaxReweight(int) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- setNMinor(int) - Method in class etomica.graphics.DeviceSlider
-
- setNMolecules(ISpecies, int) - Method in class etomica.box.Box
-
Sets the number of molecules in this box of the given Species to n.
- setNMonoAcid(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- setNMonoOl(int) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- setNo72B2B3NonAdd(boolean) - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- setNoisyAdjustment(boolean) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
- setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.g3d.Graphics3D
-
used by CartoonRenderer (DNA surface) and GeoSurfaceRenderer (face) to
assign a noisy shade to the surface it will render
- setNoisySurfaceShade(Point3i, Point3i, Point3i) - Method in class org.jmol.util.GData
-
- setNominalFluctuation(double) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- setNominalReference(IMoleculeList) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setNominalTheta(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- setNominalTheta(double) - Method in class etomica.normalmode.MeterThetaDeviation
-
- setNoOfSpheres(JTextField) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- setNoOfSteps(int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setNoOfSteps(int) - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
-
- setNormalModes(NormalModes) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setNormalModes(NormalModes) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setNormalPoint(Vector, Vector) - Method in class etomica.math.geometry.Plane
-
Defines the plane via a normal vector (1st argument) and
a point (2nd argument).
- setNormalVector(Vector) - Method in class etomica.math.geometry.Plane
-
Sets the orientation of the plane to be normal to the given vector.
- setNPoints(int) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- setnPoints(int[]) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setnReactCO(int) - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- setNRows(int) - Method in class etomica.data.types.DataTable.DataInfoTableFactory
-
Sets the number of rows.
- setNSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the post slider value changed action.
- setNSpheres(int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setNSpheres(int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setNthSpeciesAdded(int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- setNthSpeciesSelectedIndex(int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setNTicks(int) - Method in class etomica.graphics.DisplayScrollingGraph
-
- setNullPotential(PotentialHard) - Method in class etomica.integrator.IntegratorHard.Agent
-
- setNullPotential(PotentialHard, AtomType) - Method in class etomica.integrator.IntegratorHard
-
Sets the "null" potential for the given AtomType.
- setNullRegionMethod(int) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- setNullRegionMethod(int) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- setNullRegionMethod(int) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- setNumAlpha(int) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setNumAlpha(int) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setNumAlpha(int) - Method in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- setNumAlpha(int) - Method in class etomica.modules.multiharmonic.overlap.AccumulatorOverlapAverageUa2
-
- setNumAlpha(int) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setNumAlpha(int) - Method in class etomica.normalmode.MeterTargetTP
-
- setNumAlpha(int) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- setNumAlpha(int) - Method in class etomica.overlap.MeterOverlap
-
- setNumAlpha(int) - Method in class etomica.virial.overlap.AccumulatorVirialOverlapSingleAverage
-
- setNumAlpha(int) - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- setNumAlpha(int) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
Sets the number of alpha values used for the production stage of the
simulation
- setNumAlpha(int) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
Sets the number of alpha values used for the production stage of the
simulation.
- setNumAtoms(int) - Method in class etomica.chem.models.ModelChain
-
Sets the number of atoms per chain molecule.
- setNumBeads(int) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- setNumber(double) - Method in class etomica.modules.materialfracture.StrainColorScheme
-
- setNumberFraction(double[]) - Method in class etomica.species.SpeciesSpheresHetero
-
Sets the number fraction of each child atom type made by
this factory.
- setNumberOfModesChanged(int) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setNumberOfTrials(int) - Method in class etomica.models.hexane.MCMoveCBMC
-
- setNumBoxes(int) - Method in class etomica.integrator.IntegratorPT.BoxTracker
-
Specifies the number of boxes that are tracked.
- setNumCells(int) - Method in class etomica.threaded.domain.NeighborCellManagerThreaded
-
- setNumCO(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setNumCollapseBins(int) - Method in class etomica.data.history.HistoryCollapsing
-
Sets the number of "collapse" bins.
- setNumDigitColumns(int) - Method in class etomica.graphics.DisplayTable
-
- setNumEquilibrationSubsteps(int) - Method in class etomica.thermointegration.IntegratorThermodynamic
-
Sets the number of steps equilibration steps performed at each
thermodynamic state point before data collection begins.
- setNumerator(int) - Method in interface etomica.graph.model.Coefficient
-
- setNumerator(int) - Method in class etomica.graph.model.impl.CoefficientImpl
-
- setNumFactors(int) - Method in interface etomica.graph.model.Graph
-
- setNumFactors(int) - Method in class etomica.graph.model.impl.GraphImpl
-
- setNumGraft(int) - Method in class etomica.modules.colloid.ColloidSim
-
- setNumInnerSteps(int) - Method in class etomica.freeenergy.npath.IntegratorImageMultistepMD
-
- setNumLeafAtoms(int) - Method in class etomica.species.SpeciesSpheres
-
Specifies the number of child atoms in each atom constructed by this factory.
- setNumMembraneLayers(int) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setNumMembraneLayers(int) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setNumO2(int) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setNumP(int) - Method in class etomica.normalmode.MeterDDP
-
- setNumP(int) - Method in class etomica.normalmode.MeterDP
-
- setNumRawDataDoubles(int) - Method in class etomica.data.AccumulatorAverageBootstrap
-
Sets the number of times the random block generation method is used.
- setNumRawDataDoubles(int) - Method in class etomica.data.AccumulatorAverageCollapsingLog
-
Sets the number of times the random block generation method is used.
- setNumSubSteps(long) - Method in class etomica.overlap.IntegratorOverlap
-
Sets the number of total number of integrator steps the sub-integrators
perform for every step of the overlap integrator.
- setNumSubsteps(int) - Method in class etomica.thermointegration.IntegratorThermodynamic
-
Sets the number of steps performed at each thermodynamic state point.
- setNumSubSteps(int) - Method in class etomica.virial.overlap.IntegratorOverlap
-
Sets the number of total number of integrator steps the sub-integrators
perform for every step of the overlap integrator.
- setNumSurfaceSites(int) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
- setNumSurfaceSites(int) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- setNumThreads(int, Box) - Method in class etomica.threaded.atom.PotentialMasterListThreaded
-
- setNumThreads(int, Box) - Method in class etomica.threaded.domain.PotentialMasterListThreaded
-
- setNumTrial(int) - Method in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- setNumTrial(int) - Method in class etomica.virial.MCMoveClusterRingRegrow
-
Sets the number of configurational bias trials
- setNumTrial(int) - Method in class etomica.virial.MCMoveClusterRingRegrowExchange
-
Sets the number of configurational bias trials
- setNumXCells(int) - Method in class etomica.modules.sam.Sam
-
- setNumZCells(int) - Method in class etomica.modules.sam.Sam
-
- setNValues(int) - Method in class etomica.data.DataSourceUniform
-
Sets the number of uniformly spaced values.
- setOelement(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- setOffset(Vector) - Method in class etomica.config.ConformationChainLinear
-
- setOffset(Vector) - Method in class etomica.config.ConformationLinear
-
- setOffset(Vector) - Method in class etomica.modules.sam.P1Sinusoidal
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- setOmegaSquared(double[][], double[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterNMCBaskets
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setOmegaSquared(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setOmegaSquared(double[][], double[]) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setOmegaSquared(double[][]) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setOmegaSquared(double[][], double[]) - Method in class etomica.normalmode.MCMoveSingleMode
-
- setOmegaSquared(double[][]) - Method in class etomica.normalmode.MeterHarmonicEnergy
-
- setOmegaSquared(double[][]) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- setOneEVal() - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the "eigenvalues" button to its selected state.
- setOneEVal(boolean) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setOneEValButtonsVisibility(boolean) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
- setOneWV() - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the "wave vector" button to its selected state.
- setOneWV(boolean) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setOneWVButtonsVisibility(boolean) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
- setOnlyConnected(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to only generate clusters that are singly-connected.
- setOnlyDoublyConnected(boolean) - Method in class etomica.virial.cluster.ClusterGenerator
-
Set whether to only generate clusters that are doubly-connected.
- setOrderBeta(int) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- setOrientation(Vector) - Method in class etomica.config.ConformationChainLinear
-
- setOrientation(Vector) - Method in class etomica.config.ConformationLinear
-
- setOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater3P
-
- setOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater3P
-
- setOrientation(IMolecule, double[]) - Method in class etomica.models.water.OrientationCalcWater4P
-
- setOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.models.water.OrientationCalcWater4P
-
- setOrientation(IMolecule, IOrientationFull3D) - Method in interface etomica.molecule.OrientationCalc
-
Sets the orientation of the given molecule to be equal to the given
orientation.
- setOrientation(IMolecule, IOrientationFull3D) - Method in class etomica.molecule.OrientationCalcAtom
-
- setOrientation(IMolecule, double[]) - Method in interface etomica.molecule.OrientationCalcQuaternion
-
- setOrientation(IOrientationFull3D) - Method in class etomica.space3d.RotationTensor3D
-
- setOrientationCalc(ISpecies, OrientationCalc) - Method in class etomica.integrator.IntegratorRigidIterative
-
- setOrientationCalc(ISpecies, OrientationCalc) - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- setOrientationCalc(ISpecies, OrientationCalcQuaternion) - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- setOrientations(Vector[][], double[], CoordinateDefinitionHSDimer.IntegerFunction) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- setOrientationSites(AtomTypeOriented, DisplayBoxCanvasG3DSys.OrientedSite[]) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- setOrientationVectorAlpha(Space) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setOrientationVectorAlpha(Space) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setOrientationVectorBeta(Space) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setOrientationVectorBetaInitial(Space) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setOrientationVectorBetaLatticeSum(Space, double, double[][]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setOrientationVectorGamma(Space) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setOrientationVectorGamma(Space) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setOrigin(Vector) - Method in class etomica.lattice.LatticePlane
-
Sets the origin from which the position of the atom is measured.
- setOriginShift(int, int) - Method in class etomica.graphics.DisplayBox
-
Amount (in pixels) of a simple shift (translation) applied in determing origin.
- setOrtho(boolean, boolean) - Method in class etomica.dimer.IntegratorDimerRT
-
Set's the Dimer search's orthogonality criteria.
- setOtherAngles(double[]) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setOtherDensities(double[]) - Method in class etomica.normalmode.MeterDDP
-
- setOtherDensities(double[]) - Method in class etomica.normalmode.MeterDP
-
- setOtherSwitchFrac(double[]) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setOtherTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- setOtherTemperatures(double[]) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setOtherTemperatures(double[]) - Method in class etomica.normalmode.MeterTargetTP
-
- setOut(PrintStream) - Method in class etomica.data.DataSinkConsole
-
Sets the output print stream where data is written.
- setOuterGraph(Graph) - Method in class etomica.graph.iterators.CartesianIterator
-
- setOuterIterator(GraphIterator) - Method in class etomica.graph.iterators.CartesianIterator
-
- setOuterList(IAtomList) - Method in class etomica.atom.iterator.ApiInterArrayList
-
Sets the list that will be used to generate the pairs.
- setOuterList(IMoleculeList) - Method in class etomica.molecule.iterator.MpiInterArrayList
-
Sets the list that will be used to generate the pairs.
- setOuterPermutation(byte[]) - Method in class etomica.graph.iterators.CartesianPermutator
-
- setOuterPermutator(DefaultPermutator) - Method in class etomica.graph.iterators.CartesianPermutator
-
- setOverlapSplitter(DataSplitter) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- setOverwrite(boolean) - Method in class etomica.normalmode.WriteS
-
- setP1(P1ImageHarmonic) - Method in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- setP1Harmonic(P1ImageHarmonic) - Method in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- setP1Harmonic(P1ImageHarmonic) - Method in class etomica.freeenergy.npath.IntegratorImageMultistepMD
-
- setP1Harmonic(P1ImageHarmonic) - Method in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
- setPaddingSigma(double) - Method in class etomica.graphics.DisplayBox
-
Sets the amount of padding added around the edge of the drawing area.
- setPaintInterval(Box, int) - Method in class etomica.graphics.SimulationGraphic
-
setPaintInterval()
- setParameter(String, String) - Method in interface etomica.virial.GUI.models.IMolecularModel_SpeciesFactory
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setParameter(String, String) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setParameterLimits(String, double, double) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the minimum and maximum allowable values for a function parameter.
- setParameters(AtomType, ParameterSetMEAM) - Method in class etomica.meam.PotentialMEAM
-
- setParameters(String) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- setParameters(double) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- setParameters(String) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- setParameters(double) - Method in class etomica.yukawa.P2HC2Yukawa
-
Parameter calculation method.
- setParametersIMC(AtomType, ParameterSetMEAM) - Method in class etomica.meam.PotentialMEAM
-
- setParameterWrapper(ParameterBase) - Method in class etomica.util.ParseArgs
-
Sets the parameterWrapper
- setParameterWrapper(ParameterBase) - Method in class etomica.util.ReadParameters
-
Sets the parameterWrapper
- setParameterWrapper(ParameterBase) - Method in class etomica.util.WriteParameters
-
Sets the parameterWrapper
- setParams() - Method in class etomica.virial.BnJHBVArgon_Analytic
-
- setParent(IMolecule) - Method in class etomica.atom.Atom
-
Informs the Atom that the given AtomGroup is its parent.
- setParent(IMolecule) - Method in interface etomica.atom.IAtom
-
Informs the Atom that the given IMolecule is its parent.
- setParseIntegerOnly(boolean) - Method in class etomica.util.ScientificFormat
-
- setPartner(int, int) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- setPass2(boolean) - Method in class org.jmol.g3d.Graphics3D
-
- setPass2(boolean) - Method in class org.jmol.util.GData
-
- setPauseAfterEachAction(boolean) - Method in class etomica.action.activity.ActivityGroupSeries
-
- setPbcEnforcer(BoxImposePbc) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- setPbcEnforcer(BoxImposePbc) - Method in class etomica.nbr.list.NeighborListManager
-
- setPCenter(double[]) - Method in class etomica.normalmode.MeterDDP
-
- setPCenter(double[]) - Method in class etomica.normalmode.MeterDP
-
- setPeriodicity(boolean[]) - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
- setPerpendicularTo(Vector) - Method in class etomica.space3d.Vector3D
-
- setPerspectiveDepth(boolean) - Method in class g3dsys.control.G3DSys
-
- setPHarmonic(double, double) - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- setPhi(double) - Method in class etomica.models.hexane.CheckCBMCHexane
-
- setPhi(double) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
-
- setPhi(double) - Method in class etomica.potential.P4TorsionDreiding
-
- setPhongExponent(int) - Static method in class org.jmol.util.GData
-
p in I = df * (N dot L) + sf * (R dot V)^p
- setPistonPotential(P1HardMovingBoundary) - Method in class etomica.modules.pistoncylinder.BoundaryPistonCylinder
-
- setPixelUnit(Pixel) - Method in class etomica.graphics.DisplayBox
-
Sets unit for conversion between simulation units and display pixels.
- setPixelUnit(Pixel) - Method in class etomica.graphics.DisplayCanvas
-
Sets unit for conversion between simulation units and display pixels.
- setPixelUnit(Pixel) - Method in class etomica.graphics.DisplayPolytope
-
Sets unit for conversion between simulation units and display pixels.
- setPixelUnitToMillimeter(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the millimeters per pixel constant.
- setPlaneColor(Color) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Sets the color of the plane.
- setPlayDumb(boolean) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
With "play dumb" on, the bias will simply try to produce a flat
histogram based on previously-measured free energy differences
(no fitting or defect free energy will be used).
- setPolygonCount(int) - Method in class org.jmol.util.MeshSurface
-
- setPolytope(Polytope) - Method in class etomica.graphics.DisplayPolytope
-
Specifies the polytope for this display.
- setPolytopeCanvas(DisplayCanvas) - Method in class etomica.graphics.DisplayPolytope
-
- setPoreCenters(Vector[]) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- setPoreDim(int) - Method in class etomica.space.BoundaryRectangularPore
-
Sets the periodic dimension to that indicated by the given value
(0 is x-dimension, 1 is y-dimension, etc.).
- setPoreRadius(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- setPosition(IAtom, String) - Method in class etomica.config.ConfigurationFile
-
- setPosition(IAtom, String) - Method in class etomica.config.ConfigurationOrientedFile
-
- setPosition(double) - Method in class etomica.lattice.LatticePlane
-
Sets to the position of the i-th plane from the one through the origin.
- setPosition(Vector) - Method in class etomica.math.geometry.Hypersphere
-
- setPosition(Vector) - Method in class etomica.math.geometry.Polytope
-
Sets the position of the geometric center of the polytope.
- setPosition(Vector) - Method in interface etomica.math.geometry.Shape
-
Sets the position of the shape, which typically represents some central
point within it.
- setPositionDefinition(IMoleculePositionDefinition) - Method in class etomica.action.BoxImposePbc
-
- setPositionDefinition(IMoleculePositionDefinition) - Method in class etomica.data.meter.MeterProfileByAtoms
-
- setPositionDefinition(IMoleculePositionDefinition) - Method in class etomica.data.meter.MeterProfileByVolume
-
- setPositionDefinition(IMoleculePositionDefinition) - Method in class etomica.integrator.mcmove.MCMoveRotateMolecule3D
-
- setPositionDefinition(IMoleculePositionDefinition) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
-
- setPositionDefinition(IMoleculePositionDefinition) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- setPositionDefinition(IMoleculePositionDefinition) - Method in class etomica.virial.CoordinatePairMoleculeSet
-
- setPositionSource(RandomPositionSource) - Method in class etomica.data.meter.MeterProfile
-
Sets a new RandomPositionSource for this meter to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.data.meter.MeterWidomInsertion
-
Sets a new RandomPositionSource for this meter to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
Sets a new RandomPositionSource for this move to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.integrator.mcmove.MCMoveMoleculeExchange
-
Sets a new RandomPositionSource for this move to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
Sets a new RandomPositionSource for this meter to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Sets a new RandomPositionSource for this meter to use.
- setPositionSource(RandomPositionSource) - Method in class etomica.models.hexane.CBMCGrowStraightAlkane
-
- setPositivePrefix(String) - Method in class etomica.util.ScientificFormat
-
- setPositiveSuffix(String) - Method in class etomica.util.ScientificFormat
-
- setPostAction(IAction) - Method in class etomica.action.SimulationRestart
-
- setPostAction(IAction) - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- setPostAction(IAction) - Method in class etomica.graphics.Device
-
Sets an action to be performed after the primary action executed
by the device.
- setPotential(DataSourceScalar) - Method in class etomica.data.meter.MeterEnergy
-
- setPotential(IPotentialMolecular) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- setPotential(IPotentialMolecular) - Method in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- setPotential(IPotentialMolecular) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- setPotential(String) - Method in class etomica.modules.insertion.InsertionGraphic
-
- setPotential(P1HardMovingBoundary) - Method in class etomica.modules.pistoncylinder.MeterRDFCylinder
-
- setPotential(String) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- setPotential(String) - Method in class etomica.modules.swmd.SwmdGraphic
-
- setPotential(IPotentialAtomic[]) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- setPotential(IPotentialAtomic) - Method in class etomica.normalmode.MCMoveAtomCoupled
-
- setPotential(Potential2) - Method in class etomica.normalmode.MCMoveAtomSuperBox
-
- setPotential(IPotentialMolecular) - Method in class etomica.normalmode.MCMoveMoleculeCoupled
-
- setPotential(Potential2SoftSpherical) - Method in class etomica.normalmode.NormalModesPotential
-
- setPotential(Potential2SoftSpherical) - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- setPotential(PotentialGroup) - Method in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- setPotentialCalculation(PotentialCalculationEnergySum) - Method in class etomica.data.meter.MeterPotentialEnergy
-
- setPotentialCalculation(DataSourceEnergies.PotentialCalculationEnergies) - Method in class etomica.freeenergy.npath.DataSourceEnergies
-
- setPotentialCollectionFactory(ICollectionPotential) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- setPotentialGroupInterNonBondedLike(PotentialGroup) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setPotentialGroupInterNonBondedUnlike(PotentialGroup) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- setPotentialGroupIntraBonded(PotentialGroup) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setPotentialIntraBondedTorsion(IPotentialAtomic) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setPotentialJList(JList) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialJList(JList) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialList(Class[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPotentialListAtoms() - Method in class etomica.dimer.SimDimerMEAMadatom
-
- setPotentialListAtoms() - Method in class etomica.kmc.SimKMCMEAMadatom
-
- setPotentialListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialMaster(PotentialMaster) - Method in class etomica.data.meter.MeterHyperVirial
-
- setPotentialMaster(PotentialMaster) - Method in class etomica.data.meter.MeterPressure
-
- setPotentialMaster(PotentialMaster) - Method in class etomica.liquidLJ.MeterPU
-
- setPotentialMaster(PotentialMaster) - Method in class etomica.liquidLJ.MeterPUCut
-
- setPotentialMaster(PotentialMaster) - Method in class etomica.liquidLJ.MeterPUCutLS
-
- setPotentialMaster(PotentialMaster) - Method in class etomica.modules.vle.MeterPressure2
-
Sets the integrator associated with this instance.
- setPotentialMaster(PotentialMasterList) - Method in class etomica.nbr.list.BoxAgentSourceCellManagerList
-
- setPotentialMaster(PotentialMasterListMolecular) - Method in class etomica.nbr.list.molecule.BoxAgentSourceCellManagerListMolecular
-
- setPotentialMaster(PotentialMasterListMolecular) - Method in class etomica.nbr.list.molecule.NeighborCellManagerListMolecular
-
- setPotentialMaster(PotentialMasterListMolecular) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- setPotentialMaster(PotentialMasterList) - Method in class etomica.nbr.list.NeighborCellManagerList
-
- setPotentialMaster(PotentialMasterList) - Method in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- setPotentialMaster(PotentialMaster) - Method in class etomica.nbr.PotentialGroupHybrid
-
- setPotentialMaster(PotentialMaster) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setPotentialMaster(PotentialMasterList, AtomType[]) - Method in class etomica.potential.P2SquareWellRobust
-
Informs the square-well class what the potential master is (if neighbor
listing is used) and the types of atoms interacting with this potential.
- setPotentialMaster(PotentialMaster) - Method in class etomica.potential.PotentialGroup
-
- setPotentialMaster(PotentialMaster) - Method in class etomica.virial.ClusterSumExternalField
-
- setPotentialMasterDADv2(PotentialMaster) - Method in class etomica.liquidLJ.MeterPUCut
-
- setPotentialMasterDADv2(PotentialMaster) - Method in class etomica.liquidLJ.MeterPUCutLS
-
- setPotentialMasterDADv2(PotentialMaster, double[]) - Method in class etomica.normalmode.MeterSolidDACut
-
- setPotentialMC(IPotentialAtomic) - Method in class etomica.modules.colloid.NeighborListManagerColloid
-
- setPotentialMolecularNonBondedLike(IPotentialMolecular) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularLike
-
- setPotentialMolecularUnlike(IPotentialMolecular) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- setPotentialParamAndValuesString(String[][]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPotentialParamDispayTable(JTable) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialParamDispayTable(JTable) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialParamDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialParamDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialParamDisplayTM(ModelPotParamDisplayTable) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialParamDisplayTM(ModelPotParamDisplayTable) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setPotentialParamDisplayTMListener(TableModelListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setPotentialParamString(String[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPotentialPseudo(IPotentialAtomic) - Method in class etomica.modules.colloid.NeighborListManagerColloid
-
- setPotentialRange(double) - Method in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
Sets the potential range to the given value.
- setPotentialRange(double) - Method in class etomica.nbr.cell.NeighborCellManager
-
Sets the potential range to the given value.
- setPotentialsClassList(Class[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPotentialsCollectionBuilder(BuilderCollectionPotential) - Method in class etomica.virial.GUI.models.ModelSimulationConstructor
-
- setPotentialSites(String[]) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setPotentialsSelectedIndex(int[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPotentialsSelectedIndex(int, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setPreAction(IAction) - Method in class etomica.graphics.Device
-
Sets an action to be performed before the primary action executed
by the device.
- setPrecision(int) - Method in class etomica.data.types.DataDoubleBDArray.DataInfoDoubleBDArrayFactory
-
- setPrecision(int) - Method in class etomica.graphics.DecimalSlider
-
Mutator method for precision of slider.
- setPrecision(int) - Method in class etomica.graphics.DeviceBox
-
Accessor method of the precision, which specifies the number of significant figures to be displayed.
- setPrecision(int) - Method in class etomica.graphics.DeviceSlider
-
- setPrecision(int) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the precision of the scrollbar.
- setPrecision(int) - Method in class etomica.graphics.DisplayTable
-
Accessor method of the precision, which specifies the number of
significant figures to be displayed.
- setPrecision(int) - Method in class etomica.graphics.DisplayTextBox
-
Accessor method of the precision, which specifies the number of significant figures to be displayed.
- setPrecision(int) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
Accessor method of the precision, which specifies the number of significant figures to be displayed.
- setPrecision(int) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the precision of the scrollbar.
- setPrecision(int) - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
- setPrecisionLimit(int) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
-
- setPrecisionLimit(int) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- setPrefactor(double) - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- setPreferredSize(int, int) - Method in class etomica.graphics.DeviceTable
-
Set the preferred size attribute of the scrolled window the table
sits on.
- setPrefix(Prefix) - Method in class etomica.units.PrefixedUnit
-
Changes prefix to given instance if prefixAllowed flag is true.
- setPRes(double) - Method in class etomica.normalmode.MeterSolidDA
-
- setPressure(double) - Method in class etomica.association.MCMoveVolumeAssociated
-
- setPressure(double) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- setPressure(double) - Method in class etomica.data.meter.MeterWidomInsertion
-
- setPressure(double) - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- setPressure(double, double, IFunction) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setPressure(double) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
- setPressure(double) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- setPressure(double) - Method in class etomica.modules.adsorption.DataSourceDensityFunction
-
- setPressure(double) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- setPressure(double) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- setPressure(double) - Method in class etomica.normalmode.MCMoveVolumeSolid
-
- setPressure(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- setPressure(double) - Method in class etomica.normalmode.nptdemo.ColorSchemeScaledOverlap
-
- setPressure(double) - Method in class etomica.normalmode.nptdemo.DisplayBoxCanvas2DNpTScaling
-
- setPressure(double) - Method in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- setPressure(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setPrevX(float) - Method in class etomica.graphics.DisplayCanvas
-
- setPrevY(float) - Method in class etomica.graphics.DisplayCanvas
-
- setPrimitive(Primitive) - Method in class etomica.lattice.BravaisLattice
-
Sets the primitive for this lattice to the one given, and
updates the site positions.
- setPrimitive(Primitive) - Method in class etomica.lattice.LatticePlane
-
- setPrimitive(Primitive) - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- setProfileDim(int) - Method in class etomica.data.meter.MeterProfile
-
Accessor method for vector describing the direction along which the profile is measured.
- setProfileDim(int) - Method in class etomica.data.meter.MeterProfileByAtoms
-
Accessor method for vector describing the direction along which the profile is measured.
- setProfileDim(int) - Method in class etomica.data.meter.MeterProfileByVolume
-
Accessor method for vector describing the direction along which the profile is measured.
- setProfileDim(int) - Method in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- setProperty(String, String) - Method in interface etomica.graph.engine.Environment
-
- setProperty(String, String) - Method in class etomica.graph.engine.impl.EnvironmentImpl
-
- setProperty(String) - Method in class etomica.graphics.DeviceSlider
-
- setProperty(String) - Method in class etomica.graphics.DeviceSpinner
-
- SetPropertyFilter - Class in etomica.graph.operations
-
- SetPropertyFilter(Property) - Constructor for class etomica.graph.operations.SetPropertyFilter
-
- setPT2(boolean) - Static method in class etomica.potential.P2O2Bartolomei
-
- setPullFactor(double) - Method in class etomica.integrator.mcmove.MCMoveIDBiasAction
-
- setPushInterval(long) - Method in class etomica.data.DataAccumulator
-
Accumulated data are pushed to the data sinks after every pushInterval calls
to putData.
- setQ(double) - Method in class etomica.chem.electrostatics.Charge
-
- setQuadrupolarMomentSquare(double) - Method in class etomica.potential.P22CLJQ
-
- setQuadrupolarMomentSquare(double) - Method in class etomica.potential.P2LJQ
-
- setQuadrupolarMomentSquare(double) - Method in class etomica.potential.P2LJQQ
-
- setQuality(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the JPEG encoding quality.
- setQuaternions(double[]) - Method in class etomica.space3d.RotationTensor3D
-
- setQuiet(boolean) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
Sets the quiet flag, indicating if unsafe-neighbor conditions should generate
an error message (would not want this if atoms were inserted in a MC
move, for example).
- setQuiet(boolean) - Method in class etomica.nbr.list.NeighborListManager
-
Sets the quiet flag, indicating if unsafe-neighbor conditions should generate
an error message (would not want this if atoms were inserted in a MC
move, for example).
- setQuiet(boolean) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- setQuiet(boolean) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
-
- setQuiet(boolean) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- setR0(double) - Method in class etomica.potential.P2Harmonic
-
Sets the the separation at which potential is at its minimum.
- setr2d2udr2(double[]) - Method in class etomica.virial.PercusYevick1QC
-
- setRadicalColor(AtomType, Color) - Method in class etomica.modules.catalysis.ColorSchemeRadical
-
- setRadioGroupPostAction(IAction) - Method in class etomica.graphics.DeviceThermoSlider
-
Sets an action to be performed after a isothermal/adiabatic button is
pressed and the integrator's isothermality has been set.
- setRadius(double) - Method in class etomica.math.geometry.Hypersphere
-
- setRadius(double) - Method in class etomica.potential.P1SoftBoundary
-
Sets the radius.
- setRandom(IRandom) - Method in class etomica.simulation.Simulation
-
Set the simulation's random number generator to the given one.
- setRandom(IRandom) - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- setRandomCube(IRandom) - Method in interface etomica.space.Vector
-
Assigns each component to (its own) random value between -0.5 and + 0.5.
- setRandomCube(IRandom) - Method in class etomica.space1d.Vector1D
-
- setRandomCube(IRandom) - Method in class etomica.space2d.Vector2D
-
- setRandomCube(IRandom) - Method in class etomica.space3d.Vector3D
-
- setRandomCube(IRandom) - Method in class etomica.spaceNd.VectorND
-
- setRandomInSphere(IRandom) - Method in interface etomica.space.Vector
-
Assigns this vector to equal a point chosen randomly in the volume
of a unit sphere.
- setRandomInSphere(IRandom) - Method in class etomica.space1d.Vector1D
-
- setRandomInSphere(IRandom) - Method in class etomica.space2d.Vector2D
-
- setRandomInSphere(IRandom) - Method in class etomica.space3d.Vector3D
-
- setRandomInSphere(IRandom) - Method in class etomica.spaceNd.VectorND
-
- setRandomNumberGenerator(IRandom) - Method in class etomica.association.AtomSourceRandomDimer
-
- setRandomNumberGenerator(IRandom) - Method in class etomica.association.AtomSourceRandomSmer
-
- setRandomNumberGenerator(IRandom) - Method in class etomica.association.MoleculeSourceRandomDimer
-
- setRandomNumberGenerator(IRandom) - Method in class etomica.atom.AtomSourceRandomLeaf
-
Sets the random number generator used to pick atoms
- setRandomNumberGenerator(IRandom) - Method in class etomica.atom.AtomSourceRandomSpecies
-
Sets the random number generator used to pick atoms
- setRandomNumberGenerator(IRandom) - Method in class etomica.molecule.MoleculeSourceRandomMolecule
-
Sets the random number generator used to pick molecules
- setRandomSphere(IRandom) - Method in interface etomica.space.Vector
-
Assigns this vector to equal a point chosen randomly on the
surface of a unit sphere.
- setRandomSphere(IRandom) - Method in class etomica.space1d.Vector1D
-
- setRandomSphere(IRandom) - Method in class etomica.space2d.Vector2D
-
- setRandomSphere(IRandom) - Method in class etomica.space3d.Vector3D
-
Creating a random unit vector on unit sphere Uses only two random number
generator at a time
Based on M.P.
- setRandomSphere(IRandom) - Method in class etomica.spaceNd.VectorND
-
Creating a random unit vector on unit sphere Uses only two random number
generator at a time
Based on M.P.
- setRange(int[]) - Method in class etomica.lattice.RectangularLatticeNbrIteratorSquare
-
Sets the range used to define the neighboring sites.
- setRange(double, double) - Method in class etomica.meam.PotentialCuLREP
-
- setRange(double) - Method in class etomica.meam.PotentialEAM
-
- setRange(double) - Method in class etomica.meam.PotentialEAM_LS
-
- setRange(double) - Method in class etomica.meam.PotentialEFS
-
- setRange(double) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- setRange(int, double, double) - Method in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- setRange(double, double) - Method in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
-
- setRange(double) - Method in class etomica.modules.adsorption.P1Wall
-
- setRange(double) - Method in class etomica.modules.colloid.P1Wall
-
- setRange(double) - Method in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- setRange(double) - Method in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- setRange(double) - Method in class etomica.nbr.cell.PotentialMasterCell
-
- setRange(double) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
Sets the interaction range, which affects the cell-list neighbor iteration
used to generate candidate neighbors for neighbor listing.
- setRange(double) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- setRange(double) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Sets the range that determines how far to look for neighbors.
- setRange(double) - Method in class etomica.nbr.list.NeighborListManager
-
Sets the interaction range, which affects the cell-list neighbor iteration
used to generate candidate neighbors for neighbor listing.
- setRange(double) - Method in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- setRange(double) - Method in class etomica.nbr.list.PotentialMasterList
-
Sets the range that determines how far to look for neighbors.
- setRange(double) - Method in class etomica.nbr.PotentialMasterHybrid
-
- setRange(double) - Method in class etomica.potential.P2ReactionFieldDipole
-
- setRange(double) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- setRatio(double, double) - Method in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- setRawData(AccumulatorAverageBlockless.AllData) - Method in class etomica.data.AccumulatorAverageBlockless
-
- setRawData(AccumulatorAverageBlockless.AllData) - Method in class etomica.data.AccumulatorAverageBlocklessSlim
-
- setRCut(double) - Method in class etomica.potential.EwaldSummation
-
Sets a new value of rCutRealES
This will not alter values of alpha or nRealShells!
- setRCut(double) - Method in class etomica.virial.ClusterWheatleyMultibody
-
- setRCut(double) - Method in class etomica.virial.ClusterWheatleyMultibodyBD
-
- setRCut(double) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- setRCut(double) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- setrdfdr(double[]) - Method in class etomica.virial.HypernettedChain
-
- setrdfdr(double[]) - Method in class etomica.virial.PercusYevick
-
- setrdudr(double[]) - Method in class etomica.virial.PercusYevick1QC
-
- setRe(double) - Method in class etomica.potential.P2ModifiedMorse
-
- setRe(double) - Method in class etomica.potential.P2Morse
-
- setReader(ConsoleReader) - Method in interface etomica.graph.engine.Console
-
- setReader(ConsoleReader) - Method in class etomica.graph.engine.ConsoleUI
-
- setRef(Quaternion) - Method in class org.jmol.util.Quaternion
-
- setRefAvg(DataOverlap.DataSourceOverlapAvg) - Method in class etomica.overlap.DataOverlap
-
- setReferenceDataInterval(int) - Method in class etomica.normalmode.SimOverlapModule
-
- setReferenceFracSource(IntegratorOverlap.ReferenceFracSource) - Method in class etomica.overlap.IntegratorOverlap
-
Sets the DataSource that retrieves data from both boxes and provides
information to the integrator about their progress, which is used to
decide how much to sample each system.
- setReflecting(boolean[]) - Method in class etomica.lattice.IndexIteratorReflecting
-
Indicates the indexes of the elements that are subject to reflection.
- setRefPref(double, double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- setRefPref(double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- setRefPref(double, double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- setRefPref(double) - Method in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- setRefPref(double, double) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- setRefPref(double, double) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- setRefPref(double) - Method in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- setRefPref(double, double) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- setRefPref(double) - Method in class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- setRefPref(double) - Method in class etomica.normalmode.MeterSamplingHarmonic
-
- setRefPref(double) - Method in class etomica.normalmode.MeterSamplingTarget
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkBennetHarmonic
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkBennetTarget
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkTargetBennet
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkTargetUmbrella
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- setRefPref(double) - Method in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- setRefPref(double) - Method in class etomica.normalmode.SimBennet
-
- setRefPref(double) - Method in class etomica.normalmode.SimHarmonicUmbrella
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlap
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlap
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapLJ
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapLJ
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphere
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphere
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphereHCP
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- setRefPref(double, double) - Method in class etomica.normalmode.SimOverlapSSnxy
-
- setRefPref(double) - Method in class etomica.normalmode.SimOverlapSSnxy
-
- setRefPref(double) - Method in class etomica.normalmode.SimTargetUmbrella
-
- setRefPref(double) - Method in class etomica.normalmode.SimUmbrella
-
- setRefPref(double) - Method in class etomica.normalmode.SimUmbrellaSoftSphere
-
- setRefPref(double, double) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- setRefPref(double) - Method in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- setRefPref(double, double) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- setRefPref(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap
-
- setRefPref(double, double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setRefPref(double) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setRefStepFraction(double) - Method in class etomica.overlap.IntegratorOverlap
-
- setRejectable(boolean) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setRelaxAction(MoleculeAction) - Method in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- setRelaxAction(MoleculeAction) - Method in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- setRelaxationRateH(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setRelaxationRateP(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setRemove(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setRemoveSpecies1(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setRemoveSpecies2(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setRemoveSpecies3(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setRemoveSpeciesAfterAlertFlag(boolean) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setRepaintInterval(int) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- setRepaintSleep(int) - Method in class etomica.graphics.SimulationGraphic
-
- setRepeatCurrentAction(boolean) - Method in class etomica.action.activity.Controller
-
Flag indicating whether the current action should be repeated indefinitely before
moving on to the next action.
- setRescalingToFitVolume(boolean) - Method in class etomica.config.ConfigurationLattice
-
Sets the resizeLatticeToFitVolume flag, which if true indicates that the
primitive vectors should be resized to fit the dimensions of the box.
- setRescalingToFitVolume(boolean) - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice
-
Sets the resizeLatticeToFitVolume flag, which if true indicates that the
primitive vectors should be resized to fit the dimensions of the box.
- setRescalingToFitVolume(boolean) - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice
-
Sets the resizeLatticeToFitVolume flag, which if true indicates that the
primitive vectors should be resized to fit the dimensions of the box.
- setReset(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setReset(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setResetAction(IAction) - Method in class etomica.graphics.DeviceNSelector
-
- setResidual(boolean) - Method in class etomica.data.meter.MeterWidomInsertion
-
Sets flag specifying if full or residual chemical potential is computed
Default is true (only residual is computed)
- setResidual(boolean) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setResizable(boolean) - Method in class etomica.graphics.DisplayCanvas
-
- setResizable(boolean) - Method in class etomica.graphics.DisplayPolytope
-
- setResizeOnNewBox(boolean) - Method in class etomica.graphics.DisplayBox
-
Set the flag indicating whether the graphic should resize from its
currently displayed size when a new box is set.
- setRgb(Rgb16) - Method in class org.jmol.util.Rgb16
-
- setRm(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setRmax(double) - Method in class etomica.data.meter.MeterDihedralAngle
-
- setRmax(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setRmSquared(double) - Method in class etomica.potential.P2Exp6Buckingham
-
- setRotationAxis(Vector, double) - Method in class etomica.space3d.RotationTensor3D
-
Sets the tensor for rotation about the axis v by an angle theta.
- setRotationAxisCT(Vector, double) - Method in class etomica.space3d.RotationTensor3D
-
- setRotationBOTTOM(int, double) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
- setRotationMatrix(Matrix3f) - Method in class org.jmol.g3d.Graphics3D
-
- setRotationScale(Matrix3f) - Method in class org.jmol.util.Matrix4f
-
Replaces the upper 3x3 matrix values of this matrix with the values in the
matrix m1.
- setRotationTOP(int, double) - Method in class etomica.config.GrainBoundaryTiltConfiguration
-
Sets tensor for rotation about the indicated axis (0=x,1=y,2=z) by
the given angle.
- setRotNum(int) - Method in class etomica.dimer.IntegratorDimerRT
-
- setRoute(int) - Method in class etomica.action.IntegratorDimerApproach
-
- setRoute(boolean) - Method in class etomica.virial.HypernettedChain
-
- setRoute(boolean) - Method in class etomica.virial.PercusYevick
-
- setRouteParams(double[][]) - Method in class etomica.action.IntegratorDimerApproach
-
- setRow(int, float, float, float) - Method in class org.jmol.util.Matrix3f
-
Sets the specified row of this matrix3d to the three values provided.
- setRow(int, float[]) - Method in class org.jmol.util.Matrix4f
-
Sets the specified row of this matrix4f to the four values provided.
- setRowA(int, float[]) - Method in class org.jmol.util.Matrix3f
-
Sets the specified row of this matrix3d to the four values provided.
- setRowHeaders(String[]) - Method in class etomica.data.types.DataTable.DataInfoTableFactory
-
Sets the row headers.
- setRowLabelColumnHeader(String) - Method in class etomica.graphics.DisplayTable
-
Sets the header of the row-label column.
- setRowLabels(String[]) - Method in class etomica.graphics.DisplayTable
-
Sets values for descriptive text for each row (as defined before
transpose).
- setRowV(int, Vector3f) - Method in class org.jmol.util.Matrix3f
-
Sets the specified row of this matrix3d to the Vector provided.
- setRPow(double) - Method in class etomica.virial.MCMoveClusterAtomDiscrete
-
- setRun(JButton) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setRun(JButton) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setS(int) - Static method in class etomica.potential.P2O2Bartolomei
-
- setSafetyFactor(double) - Method in class etomica.nbr.CriterionPositionWall
-
Sets the safety factor (between 0 and 1.0) that determines when the
criterion thinks it needs an update.
- setSafetyFactor(double) - Method in class etomica.nbr.CriterionSimple
-
- setSafetyFactor(double) - Method in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
Sets the safety factor.
- setSafetyFactor(double) - Method in class etomica.nbr.list.PotentialMasterList
-
Sets the safety factor.
- setSafetyFactor(double) - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- setSameFileEachTime(boolean) - Method in class etomica.data.DataLogger
-
Write to the same file at each time INTERVAL, and close the file at the
end of the simulation.
- setSampleClusters(ClusterWeight[]) - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
- setSampledSwitchFrac(double) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setSaveValues(JButton) - Method in class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- setScale(double) - Method in class etomica.action.BoxInflate
-
Sets the scale defining the amount of inflation.
- setScale(double) - Method in class etomica.graphics.DisplayBox
-
- setScale(double) - Method in class etomica.graphics.DisplayPolytope
-
- setScale(float) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to a scale matrix with the passed scale
amount.
- setSCF(boolean) - Method in class etomica.potential.P2QChemInterpolated
-
- setSearchLimit(int) - Method in class etomica.kmc.IntegratorKMC
-
- setSecurityOff(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets whether or not scripts should be run securely
- setSeed(int) - Method in class etomica.util.random.RandomMersenneTwister
-
Configures the RNG with the given seed.
- setSeedArray(int[]) - Method in class etomica.util.random.RandomMersenneTwister
-
Configures the RNG with an array of seeds
- setSeeds(int[]) - Method in class etomica.virial.simulations.SimulationVirial
-
- setSeen(int) - Method in class etomica.graph.traversal.AbstractTraversal
-
- setSelected(String) - Method in class etomica.graphics.DeviceButtonGroup
-
Selects the button with the given label.
- setSelected(int) - Method in class etomica.graphics.DeviceButtonGroup
-
Selects ith radio button.
- setSelected(int) - Method in class etomica.graphics.DeviceSelector
-
Sets the i-th item (counting from 0) in the list as the one currently selected.
- setSelected(int) - Method in class etomica.graphics.DeviceThermoSelector
-
Sets the i-th item (counting from 0) in the list as the one currently selected.
- setSelectedFloats(float, BitSet, float[]) - Static method in class org.jmol.util.Parser
-
- setSelectedSpecies(IMolecularModel_SpeciesFactory) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSelectedValue(int, ScriptVariable) - Method in class org.jmol.script.ScriptVariable
-
- setSfacPlotSink(IDataSink) - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- setShakeTolerance(double) - Method in class etomica.integrator.IntegratorVelocityVerletShake
-
- setShape(Polytope) - Method in class etomica.data.meter.MeterLocalDensity
-
- setShape(Polytope) - Method in class etomica.data.meter.MeterLocalMoleFraction
-
Sets the subvolume shape for the mole fraction calculation.
- setShape(String) - Method in class etomica.graphics.DeviceTrioControllerButton
-
Sets display shape of the device.
- setShapeOrigin(Vector) - Method in class etomica.data.meter.MeterLocalMoleFraction
-
Sets the origin of the subvolume (Polytopes typically have their center
at 0).
- setShearRateNumber(double) - Method in class etomica.modules.rheology.IntegratorPolymer
-
- setShift(Vector) - Method in class etomica.interfacial.WriteConfigurationInterfacial
-
- setShiftX(float) - Method in class etomica.graphics.DisplayCanvas
-
- setShiftY(float) - Method in class etomica.graphics.DisplayCanvas
-
- setShowBorder(boolean) - Method in class etomica.graphics.DeviceSlider
-
- setShowBorder(boolean) - Method in class etomica.graphics.DeviceSpinner
-
- setShowBoundary(boolean) - Method in class etomica.graphics.DisplayBox
-
Set the flag indicating if the boundary should be drawn.
- setShowEValvalues(boolean) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set whether the eigenvalue # text box should be displayed.
- setShowingColumnHeaders(boolean) - Method in class etomica.graphics.DisplayTable
-
- setShowingRowLabels(boolean) - Method in class etomica.graphics.DisplayTable
-
Mutator method for whether table should include a column of "x" values.
- setShowingUnits(boolean) - Method in class etomica.graphics.DisplayTable
-
Flag indicating whether a units suffix applied to the column headers (or
row labels, if transposing).
- setShowSlider(boolean) - Method in class etomica.graphics.DeviceSlider
-
- setShowValues(boolean) - Method in class etomica.graphics.DeviceSlider
-
- setShowValues(boolean) - Method in class etomica.graphics.DeviceThermoSlider
-
Set whether the temperature text box should be displayed.
- setShowValues(boolean) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set whether the temperature text box should be displayed.
- setShowValues(boolean) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set whether the x- and y-Cell # text box should be displayed.
- setShowValues(boolean) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set whether the wavevector # text box should be displayed.
- setSigma(double) - Method in class etomica.graphics.ColorSchemeOverlap
-
- setSigma(double) - Method in class etomica.modules.adsorption.EOSSW
-
- setSigma(double) - Method in class etomica.modules.adsorption.P1Wall
-
- setSigma(double) - Method in class etomica.modules.colloid.P1Wall
-
- setSigma(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
Sets the radius.
- setSigma(double) - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
Sets the radius.
- setSigma(double) - Method in class etomica.modules.sam.P1WCAWall
-
Sets the radius.
- setSigma(double) - Method in class etomica.modules.vle.VLESim
-
- setSigma(double) - Method in class etomica.potential.P1HardPeriodic
-
- setSigma(double) - Method in class etomica.potential.P22CLJQ
-
- setSigma(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
- setSigma(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeReference
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for Lennard-Jones size parameter
- setSigma(double) - Method in class etomica.potential.P2HSDipole
-
- setSigma(double) - Method in class etomica.potential.P2LennardJones
-
Mutator method for Lennard-Jones size parameter.
- setSigma(double) - Method in class etomica.potential.P2LennardJonesDreiding
-
Mutator method for Lennard-Jones size parameter.
- setSigma(double) - Method in class etomica.potential.P2LJDipole
-
- setSigma(double) - Method in class etomica.potential.P2LJQ
-
- setSigma(double) - Method in class etomica.potential.P2LJQQ
-
- setSigma(double) - Method in class etomica.potential.P2SoftSphere
-
Mutator method for soft sphere size parameter.
- setSigma(double) - Method in class etomica.potential.P2WCA
-
Mutator method for Lennard-Jones size parameter.
- setSigma(double) - Method in class etomica.rotation.P2LJDipole
-
- setSigma(double) - Method in class etomica.units.systems.LJ
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setSigma(double, int) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setSigma(double) - Method in class etomica.virial.MayerEHardSphere
-
Sets the HS diameter.
- setSigma(double) - Method in class etomica.virial.MayerHardSphere
-
Sets the HS diameter.
- setSigma(double) - Method in class etomica.yukawa.P2HC2Yukawa
-
- setSigmaColloid(double) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setSigmaHSRef(double, int) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelEMP2_SpeciesCO2
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelLJ_SpeciesLJ
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelLJQ_SpeciesLJ
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelSPCE_SpeciesH2O
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setSigmaHSRef(double) - Method in class etomica.virial.GUI.models.MolecularModelTrappe_SpeciesCO2
-
- setSigmaHSRefField(JTextField, int) - Method in class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- setSigmaMonomer(double) - Method in class etomica.modules.colloid.ConfigurationColloid
-
- setSimEnvController(ControllerSimEnvironmentSelection) - Method in class etomica.virial.GUI.controllers.ControllerSpeciesSelection
-
- setSimulation(Simulation, Space) - Method in class etomica.action.SimulationActionAdapter
-
- setSimulation(Simulation, Space, Controller) - Method in class etomica.graphics.DeviceTrioControllerButton
-
Sets the controller that is toggled by this device.
- setSite(int[]) - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Identifies the site whose neighbors will be given on iteration.
- setSite(String) - Method in enum etomica.virial.GUI.models.EnumSiteName
-
- setSiteFactor(double) - Method in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- setSitesOnSpecies(String[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSize(int, int) - Method in class etomica.graphics.DeviceTable
-
Set the size attribute of the scrolled window the table sits on.
- setSize(int, int) - Method in class etomica.graphics.DisplayPlot
-
Sets the drawn size of the plot
- setSize(int, int) - Method in class etomica.graphics.DisplayPolytope
-
- setSize(double[]) - Method in class etomica.lattice.crystal.Primitive
-
Sets the length of each primitive vector to the corresponding
value in the given array.
- setSize(int[]) - Method in interface etomica.lattice.FiniteLattice
-
Sets the array size, defined as described in the getSize method.
- setSize(int) - Method in class etomica.lattice.IndexIteratorRectangular
-
Sets range of all indexes to the given value
Indices returned vary from 0 to size-1
- setSize(int[]) - Method in class etomica.lattice.IndexIteratorRectangular
-
Sets the individual ranges for the elements of the returned
array.
- setSize(int[]) - Method in interface etomica.lattice.IndexIteratorSizable
-
Specifies maximum index in each dimension (for dimension
i, maximum index is size[i]-1).
- setSize(int[]) - Method in class etomica.lattice.RectangularLattice
-
Sets the number lattice size (specified via the largest index in each dimension), and
rebuilds the all sites using the site factory.
- setSize(int, int) - Method in class etomica.modules.clustergenerator.Plot
-
Sets width and height of plot in pixels.
- setSize(int[]) - Method in interface g3dsys.control.IndexIterator
-
Sets the size of each dimension; in general they should all be the
same size.
- setSize(int) - Method in class org.jmol.util.Quadric
-
- setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
Sets A to the given value and B to 2.0/sqrt(3.0)*A
- setSizeA(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setSizeAB(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- setSizeAB(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- setSizeAB(double) - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- setSizeABC(double) - Method in class etomica.lattice.crystal.PrimitiveCubic
-
Sets the length of all primitive vectors to the given value.
- setSizeB(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- setSizeB(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- setSizeB(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- setSizeC(double) - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- setSlab(double) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
Set slab percentage
- setSlab(double) - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
Set slab percentage
- setSlab(int) - Method in class org.jmol.util.GData
-
clipping from the front and the back
- setSlab(BitSet, BitSet, String, String, float) - Method in class org.jmol.util.MeshSurface
-
- setSlabEnabled(boolean) - Method in class g3dsys.control.TransformManager
-
Enable/disable slab and depth
- setSlabPercent(float) - Method in class g3dsys.control.G3DSys
-
- setSleepPeriod(int) - Method in class etomica.action.activity.ActivityIntegrate
-
Sets amount of time that thread is kept in sleep state after
each doStep done on integrator.
- setSliderMajorValues(int) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the number of "major" values that should be shown on the
temperature slider.
- setSliderMajorValues(int) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the number of "major" values that should be shown on the
temperature slider.
- setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
Set the number of "major" values that should be shown on the
n- CellNum slider.
- setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the number of "major" values that should be shown on the
x- and y- CellNum slider.
- setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the number of "major" values that should be shown on the
eigenvalue slider.
- setSliderMajorValues(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the number of "major" values that should be shown on the
temperature slider.
- setSliderMinorValues(int) - Method in class etomica.graphics.DeviceThermoSlider
-
- setSliderPostAction(IAction) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the post slider value changed action.
- setSliderPostAction(IAction) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the post slider value changed action.
- setSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceEigenvaluesSlider
-
Set the post slider value changed action.
- setSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the post slider value changed action.
- setSliderTextboxesEditable(boolean) - Method in class etomica.graphics.DevicePlotPoints
-
- setSliderValueShape(String) - Method in class etomica.graphics.DeviceSlider
-
- setSliderVerticalOrientation(boolean) - Method in class etomica.graphics.DeviceSlider
-
- setSlitDim(int) - Method in class etomica.space.BoundaryRectangularSlit
-
Sets the non-periodic dimension to that indicated by the given value
(0 is x-dimension, 1 is y-dimension, etc.).
- setSmoothedY(double[]) - Method in class etomica.math.numerical.AkimaSplineSmoother
-
- setSnapshotTime(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the document time to seek to before rasterizing.
- setSoluteMoleFraction(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSoluteMoleFraction(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSolutionChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSolutionChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSolventChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSolventChamberDensity(double) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSolventThermoFrac(double) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
Sets the fraction of well energy that is gained by an atom pair when
they hop in their well.
- setSources(String[]) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the list of individual SVG sources.
- setSpace(Space) - Method in class etomica.data.types.DataTensor.DataInfoTensorFactory
-
Sets the Space
- setSpace(Space) - Method in class etomica.data.types.DataVector.DataInfoVectorFactory
-
Sets the Space
- setSpacePosition(double) - Method in class etomica.lattice.LatticePlane
-
Sets the position of the plane to be the given distance from the
origin in the direction of the normal.
- setSpecies(ISpecies) - Method in class etomica.atom.AtomSourceRandomSpecies
-
- setSpecies(ISpecies) - Method in class etomica.atom.AtomType
-
Informs the atom type what species contains the atom types.
- setSpecies(ISpecies) - Method in class etomica.data.DataSourcePositionedBoltzmannFactor
-
Sets the ISpecies for which the chemical potential is to be measured.
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterDensity
-
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterLocalMoleFraction
-
Accessor method to set which species mole-fraction or molar-density is averaged
To set to total number density, invoke with static ALL_SPECIES field as argument
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterMoleFraction
-
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterNMolecules
-
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterProfileByAtoms
-
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterProfileByVolume
-
- setSpecies(ISpecies) - Method in class etomica.data.meter.MeterWidomInsertion
-
Sets the species, takes a prototype molecule, and gets handle to
appropriate species agent in box
- setSpecies(ISpecies[]) - Method in class etomica.dimer.PotentialMasterListDimer
-
- setSpecies(ISpecies) - Method in class etomica.graphics.DeviceNSelector
-
- setSpecies(ISpecies) - Method in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- setSpecies(ISpecies[]) - Method in class etomica.integrator.mcmove.MCMoveSemigrand
-
Mutator method for the set of species that can participate in an exchange move.
- setSpecies(ISpecies) - Method in class etomica.interfacial.WriteConfigurationInterfacial
-
- setSpecies(ISpecies) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
Sets the species, takes a prototype molecule, and gets handle to
appropriate species agent in box
- setSpecies(ISpecies) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
Sets the species, takes a prototype molecule, and gets handle to
appropriate species agent in box
- setSpecies(ISpecies, ISpecies) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setSpecies(ISpecies) - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- setSpecies(ISpecies) - Method in class etomica.models.nitrogen.P0LatticeEnergyCorrec
-
- setSpecies(ISpecies) - Method in class etomica.modules.adsorption.MyMCMove
-
- setSpecies(ISpecies, ISpecies) - Method in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
-
- setSpecies(ISpecies[]) - Method in class etomica.modules.chainequilibrium.MeterConversion
-
- setSpecies(ISpecies) - Method in class etomica.modules.dcvgcmd.MyMCMove
-
- setSpecies(String) - Method in class etomica.modules.joulethomson.JouleThomson.SpeciesChooser
-
- setSpecies(ISpecies[]) - Method in class etomica.modules.rosmosis.MeterFlux
-
- setSpecies(ISpecies, ISpecies) - Method in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- setSpecies(ISpecies) - Method in class etomica.normalmode.DeviceCellNum3DSlider
-
- setSpecies(ISpecies) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- setSpecies(ISpecies, int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterAngleBend
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterRotateCH3
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- setSpecies(ISpecies) - Method in class etomica.virial.MCMoveClusterWiggleMulti
-
- setSpecies1(ISpecies) - Method in class etomica.config.ConfigurationZincblende
-
- setSpecies1AtomicFlag(boolean) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- setSpecies2(ISpecies) - Method in class etomica.config.ConfigurationZincblende
-
- setSpecies2AtomicFlag(boolean) - Method in class etomica.virial.GUI.components.BuilderCollectionPotential
-
- setSpeciesA(ISpecies, ISpecies) - Method in class etomica.config.GrainBoundaryConfiguration
-
- setSpeciesA(ISpecies) - Method in class etomica.modules.reactionequilibrium.MeterDimerFraction
-
- setSpeciesAllocation(ISpecies, float) - Method in class etomica.config.ConfigurationLatticeWithPlane
-
Sets the initial allocation of the species on the left side
of the plane.
- setSpeciesAlreadyAdded(boolean, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSpeciesB(ISpecies, ISpecies) - Method in class etomica.config.GrainBoundaryConfiguration
-
- setSpeciesColloid(ISpecies) - Method in class etomica.modules.colloid.NeighborListManagerColloid
-
- setSpeciesCount1(JTextField) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesCount2(JTextField) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesCount3(JTextField) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesDataModel(IMolecularModel_SpeciesFactory, int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- setSpeciesDM(ModelSelectedSpecies) - Method in class etomica.virial.GUI.controllers.ControllerAlkaneLengthSelection
-
- setSpeciesID(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesCO2
-
- setSpeciesID(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesEthane
-
- setSpeciesID(int) - Method in class etomica.virial.GUI.models.MolecularModel2CLJQ_SpeciesLJ
-
- setSpeciesIdentifier(String, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSpeciesIndex(int) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicLike
-
- setSpeciesIndex(int[]) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- setSpeciesIndex(int, int) - Method in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- setSpeciesIndex(int) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularLike
-
- setSpeciesIndex(int[]) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- setSpeciesIndex(int, int) - Method in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- setSpeciesInteractionIndex(int[][]) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- setSpeciesJList(JList) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesJList(JList) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesJListListener(ListSelectionListener) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setSpeciesListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.models.ViewSpeciesSelection
-
- setSpeciesListDisplayLSM(ListSelectionModel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setSpeciesMembrane(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSpeciesMembrane(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSpeciesMoleculeCount(int, int) - Method in class etomica.virial.GUI.models.ModelSelectedSpecies
-
- setSpeciesMonomer(ISpecies) - Method in class etomica.modules.colloid.NeighborListManagerColloid
-
- setSpeciesRemovalMsgBox(JOptionPane) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setSpeciesSelectedIndex(int[]) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSpeciesSelectedIndex(int, int) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSpeciesSelectionChanged(boolean) - Method in class etomica.virial.GUI.models.ModelSpeciesSelection
-
- setSpeciesSelectionDM(ModelSpeciesSelection) - Method in class etomica.virial.GUI.models.ModelAlertMsgDialog
-
- setSpeciesSolute(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSpeciesSolute1(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSpeciesSolute2(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSpeciesSolvent(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembrane
-
- setSpeciesSolvent(ISpecies) - Method in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- setSpeciesSpheres(SpeciesSpheresMono[]) - Method in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
-
- setSpeciesTube(SpeciesTube) - Method in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
-
- setSpecular(boolean) - Static method in class org.jmol.util.GData
-
- setSpecularExponent(int) - Static method in class org.jmol.util.GData
-
log_2(p) in I = df * (N dot L) + sf * (R dot V)^p for faster calculation of
shades
- setSpecularPercent(int) - Static method in class org.jmol.util.GData
-
sf in I = df * (N dot L) + sf * (R dot V)^p not a percent of anything,
really
- setSpecularPower(int) - Static method in class org.jmol.util.GData
-
fractional distance to white for specular dot
- setSpiffiness(int) - Method in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- setSpinnerPanel(JPanel) - Method in class etomica.virial.GUI.views.ViewSpeciesSelection
-
- setSpringConstant(double) - Method in class etomica.modules.materialfracture.P1Tension
-
- setSpringConstant(double) - Method in class etomica.potential.P1Harmonic
-
- setSpringConstant(double) - Method in class etomica.potential.P1HarmonicSite
-
- setSpringConstant(double) - Method in class etomica.potential.P2Anharmonic
-
Accessor method for harmonic energy parameter
- setSpringConstant(double) - Method in class etomica.potential.P2Harmonic
-
Accessor method for harmonic energy parameter
- setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setSpringConstants(double[][]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setStart(Object) - Method in class etomica.data.DataStreamAction
-
- setStart(float, float, float) - Method in class g3dsys.images.Line
-
- setStartAtom(int) - Method in class etomica.virial.MCMoveClusterAtomMulti
-
- setStartConnection(int) - Method in class etomica.virial.cluster.ClusterGenerator
-
- setStartMolecule(int) - Method in class etomica.virial.MCMoveClusterMoleculeMulti
-
- setState(boolean) - Method in class etomica.graphics.DeviceCheckBox
-
Sets the button to the given state.
- setState(boolean) - Method in class etomica.graphics.DeviceToggleButton
-
Toggles the button to the given state.
- setState(boolean) - Method in class etomica.graphics.DeviceToggleRadioButtons
-
Sets the button to the given state.
- setStationary(boolean) - Method in class etomica.potential.P1HardMovingBoundary
-
- setStatus(StatusAction.Status) - Method in class etomica.server.representations.StatusAction
-
- setStepFactor(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- setStepFreq0(double) - Method in class etomica.virial.overlap.IntegratorOverlap
-
- setStepSize(double) - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- setStepSize(double) - Method in class etomica.integrator.mcmove.MCMoveStep
-
- setStepSize(double) - Method in interface etomica.integrator.mcmove.MCMoveStepDependent
-
Sets the step size of the move.
- setStepSizeMax(double) - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- setStepSizeMax(double) - Method in class etomica.integrator.mcmove.MCMoveStep
-
- setStepSizeMax(double) - Method in interface etomica.integrator.mcmove.MCMoveStepDependent
-
Sets the maximum allowable step size.
- setStepSizeMin(double) - Method in class etomica.integrator.mcmove.MCMoveBoxStep
-
- setStepSizeMin(double) - Method in class etomica.integrator.mcmove.MCMoveStep
-
- setStepSizeMin(double) - Method in interface etomica.integrator.mcmove.MCMoveStepDependent
-
Returns the maximum allowable steps size.
- setStiffness(double, P1IntraMolecular) - Method in class etomica.virial.MCMoveChangeBondLength
-
- setStiffness(double, double) - Method in class etomica.virial.MCMoveClusterRingRegrowOrientation
-
Set PI harmonic spring stiffness for given temperature and atomic mass.
- setStopConnection(int) - Method in class etomica.virial.cluster.ClusterGenerator
-
- setStopSimulation(boolean) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setStreamAction(DataStreamAction) - Method in class etomica.action.SimulationDataAction
-
- setSubDataInfo(IDataInfo[]) - Method in class etomica.data.types.DataGroup.DataInfoGroupFactory
-
- setSubtractComb(boolean) - Method in class etomica.normalmode.DataSourceFE
-
If true, the free energy differences will not include the combinatoric
contributions (they will be the free energy of defect formation).
- setSulfurType(AtomType) - Method in class etomica.modules.sam.IntegratorVelocityVerletSAM
-
- setSum(int) - Method in class etomica.math.discrete.FixedSumIterator
-
Specifies the target sum that defines the iterates.
- setSuppressBoxLengthWarning(boolean) - Method in class etomica.nbr.cell.NeighborCellManager
-
- setSurfaceColor(Color) - Method in class etomica.modules.droplet.ColorSchemeDropletSurface
-
- setSurfaceDimension(int) - Method in class etomica.data.DataProcessorInterfacialTension
-
Sets the dimension of the surfaces.
- setSurfaceYOffset(double) - Method in class etomica.modules.catalysis.ConfigurationCatalysis
-
- setSurfaceYOffset(double) - Method in class etomica.modules.sam.ConfigurationSAM
-
- setSwitch(boolean) - Method in class etomica.models.nitrogen.PRotConstraint
-
- setSwitchFac(double) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- setSwitchFac(double) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- setSystemSigmaHSRef(double) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setT(Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the value of the Tuple3f argument.
- setT(Tuple3i) - Method in class org.jmol.util.Tuple3i
-
Sets the value of this tuple to the value of tuple t1.
- setT1(double) - Method in class etomica.normalmode.HTTPSoftSphereApplet
-
- setT2(double) - Method in class etomica.normalmode.HTTPSoftSphereApplet
-
- setTA(Tuple3f, float) - Method in class org.jmol.util.Quaternion
-
q = (cos(theta/2), sin(theta/2) * n)
- setTableColumnNames(String[]) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the column headers to the given strings and fires an event
indicating the column headers have been changed.
- setTableUpdateInterval(int) - Method in class etomica.data.DataTableAverages
-
Sets the interval for updating the table.
- setTags(DataTag[]) - Method in class etomica.data.DataInfoFactory
-
- setTags(DataTag[]) - Method in interface etomica.data.IDataInfoFactory
-
Sets the factory's tags to those in the given array.
- setTarget(IAtom) - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.ANIntergroupExchange
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.ANIntragroupExchange
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.ApiIndexList
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.ApiIntergroup
-
Specifies a target atom, which should appear in all iterates.
- setTarget(IAtom) - Method in class etomica.atom.iterator.ApiIntragroup
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
Sets the target of iteration...
- setTarget(IAtom) - Method in class etomica.atom.iterator.AtomIteratorBasis
-
Method to specify a target atom.
- setTarget(IAtom) - Method in class etomica.atom.iterator.AtomIteratorBasisAdjustableStart
-
Method to specify a target atom.
- setTarget(IAtom) - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
Sets the target of iteration...
- setTarget(IAtom) - Method in interface etomica.atom.iterator.AtomsetIteratorTargetable
-
- setTarget(IAtom) - Method in class etomica.atom.iterator.TripletInnerSequential
-
- setTarget(IAtom) - Method in class etomica.data.meter.MeterPotentialEnergy
-
- setTarget(IMolecule) - Method in class etomica.data.meter.MeterPotentialEnergy
-
- setTarget(IMolecule) - Method in class etomica.molecule.iterator.MoleculeIteratorAll
-
Sets the target of iteration...
- setTarget(IMolecule) - Method in class etomica.molecule.iterator.MoleculeIteratorMolecule
-
Specifies molecule returned by this iterator, as the one containing
the given target atom.
- setTarget(IMolecule) - Method in interface etomica.molecule.iterator.MoleculesetIteratorTargetable
-
- setTarget(IMolecule) - Method in class etomica.molecule.iterator.MpiInterspecies1A
-
Sets the target molecule with which all pairs are formed.
- setTarget(IMolecule) - Method in class etomica.molecule.iterator.MpiIntraspecies1A
-
Sets the target molecule with which all pairs are formed.
- setTarget(IMolecule) - Method in class etomica.molecule.iterator.MpiMolecule
-
Sets target atoms and determines the pair iterator according to the value
of targetAtom.
- setTarget(IAtom) - Method in class etomica.nbr.cell.Api1ACell
-
Sets the target molecule with which all pairs are formed.
- setTarget(IMolecule) - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
Sets the target molecule with which all pairs are formed.
- setTarget(IAtom) - Method in class etomica.nbr.site.Api1ASite
-
Sets the target molecule with which all pairs are formed.
- setTarget(IAtom) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- setTarget(IMolecule) - Method in class etomica.normalmode.SimEinStep2.MeterPotentialEnergyComposite
-
- setTarget(IAtom) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- setTarget(IMolecule) - Method in class etomica.normalmode.SimEinStep2HCP.MeterPotentialEnergyComposite
-
- setTarget(IAtom) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- setTarget(IMolecule) - Method in class etomica.normalmode.SimOverlapSoftSphereEin.MeterPotentialEnergyComposite
-
- setTarget(IAtom) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- setTarget(IMolecule) - Method in class etomica.normalmode.SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite
-
- setTarget(IAtom) - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- setTarget(IMolecule) - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- setTargetAtom(IAtom) - Method in interface etomica.potential.IPotential0Lrc
-
Informs the potential of a target atom.
- setTargetAtom(IAtom) - Method in class etomica.potential.IteratorDirective
-
- setTargetAtom(IAtom) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- setTargetAtom(IAtom) - Method in class etomica.potential.Potential0Lrc
-
- setTargetAvg(DataOverlap.DataSourceOverlapAvg) - Method in class etomica.overlap.DataOverlap
-
- setTargetDataInterval(int) - Method in class etomica.normalmode.SimOverlapModule
-
- setTargetDensity(double) - Method in class etomica.action.BoxInflate
-
Sets the action to change the box dimensions isotropically to achieve
the given density.
- setTargetH(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setTargetMolecule(IMolecule) - Method in interface etomica.potential.IPotential0Lrc
-
Informs the potential of a target atom.
- setTargetMolecule(IMolecule) - Method in interface etomica.potential.IPotential0MoleculeLrc
-
Informs the potential of a target atom.
- setTargetMolecule(IMolecule) - Method in class etomica.potential.IteratorDirective
-
- setTargetMolecule(IMolecule) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- setTargetMolecule(IMolecule) - Method in class etomica.potential.Potential0Lrc
-
- setTargetP(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setTargetT(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setTemp(double) - Method in class etomica.integrator.IntegratorConNVT
-
- setTemperature(double) - Method in class etomica.action.AtomActionRandomizeVelocity
-
- setTemperature(double) - Method in class etomica.action.BoxQuench
-
Sets the quench temperature.
- setTemperature(double) - Method in class etomica.action.BoxRandomizeMomenta
-
- setTemperature(double) - Method in class etomica.action.BoxScaleMomenta
-
- setTemperature(double) - Method in class etomica.data.meter.MeterHyperVirial
-
- setTemperature(double) - Method in class etomica.data.meter.MeterPressure
-
- setTemperature(double) - Method in class etomica.data.meter.MeterPressureTensor
-
- setTemperature(double) - Method in class etomica.data.meter.MeterWidomInsertion
-
- setTemperature(double) - Method in class etomica.densityofstate.DataProcessorPhi
-
- setTemperature(double) - Method in class etomica.gaussianwork.MeterBoltzmannA
-
- setTemperature(double) - Method in class etomica.gaussianwork.MeterBoltzmannB
-
- setTemperature(double) - Method in class etomica.gaussianwork.MeterWorkABandReweighting
-
- setTemperature(double) - Method in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- setTemperature(double) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the current value for the temperature slider/text box.
- setTemperature(double) - Method in class etomica.integrator.IntegratorBox
-
- setTemperature(double) - Method in class etomica.integrator.IntegratorHard
-
- setTemperature(double) - Method in class etomica.integrator.IntegratorManagerMC
-
Sets the temperature for this integrator if that's relevant
- setTemperature(double) - Method in class etomica.integrator.IntegratorMD
-
- setTemperature(double) - Method in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- setTemperature(double) - Method in class etomica.liquidLJ.MeterPU
-
- setTemperature(double) - Method in class etomica.liquidLJ.MeterPUCut
-
- setTemperature(double) - Method in class etomica.liquidLJ.MeterPUCutLS
-
- setTemperature(double) - Method in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- setTemperature(double) - Method in class etomica.liquidLJ.MeterWidomInsertionP
-
- setTemperature(double, Potential2SoftSpherical) - Method in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- setTemperature(double, Potential2SoftSpherical) - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- setTemperature(double, Potential2SoftSpherical) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- setTemperature(double, P2SoftSphericalTruncated) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- setTemperature(double) - Method in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- setTemperature(double) - Method in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setTemperature(double) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setTemperature(double) - Method in class etomica.modules.adsorption.EOSSW
-
- setTemperature(double) - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setTemperature(double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setTemperature(double) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the current value for the temperature slider/text box.
- setTemperature(double) - Method in class etomica.normalmode.BoltzmannProcessor
-
- setTemperature(double) - Method in class etomica.normalmode.DataProcessorBoltzmannFactor
-
- setTemperature(double) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveEinsteinCrystal
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveSingleMode
-
- setTemperature(double) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
Sets the temperature being sampled.
- setTemperature(double) - Method in class etomica.normalmode.MCMoveVolumeSolid
-
Sets the temperature being sampled.
- setTemperature(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
Sets the temperature being sampled.
- setTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannHarmonic
-
- setTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannHTTP
-
- setTemperature(double) - Method in class etomica.normalmode.MeterBoltzmannTarget
-
- setTemperature(double) - Method in class etomica.normalmode.MeterDDP
-
- setTemperature(double) - Method in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- setTemperature(double) - Method in class etomica.normalmode.MeterDP
-
- setTemperature(double) - Method in class etomica.normalmode.MeterOverlapSwitch
-
- setTemperature(double) - Method in class etomica.normalmode.MeterSolidDA
-
- setTemperature(double) - Method in class etomica.normalmode.MeterSolidDACut
-
- setTemperature(double) - Method in class etomica.normalmode.MeterSolidMirror
-
- setTemperature(double) - Method in class etomica.normalmode.MeterTargetTP
-
- setTemperature(double) - Method in class etomica.normalmode.MeterWorkHarmonicBennet
-
- setTemperature(double) - Method in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- setTemperature(double) - Method in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- setTemperature(double) - Method in interface etomica.normalmode.NormalModes
-
Set the temperature used for calculating omega-squared.
- setTemperature(double) - Method in class etomica.normalmode.NormalModes1DHR
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModes2D
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModes3D
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModesFromFile
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModesMolecular
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModesPotential
-
- setTemperature(double) - Method in class etomica.normalmode.NormalModesSoftSpherical
-
- setTemperature(double) - Method in class etomica.normalmode.WriteS
-
- setTemperature(double) - Method in class etomica.paracetamol.NormalModesPotentialParacetamol
-
- setTemperature(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- setTemperature(double) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
-
- setTemperature(double) - Method in class etomica.potential.P2LJDipole
-
Sets the temperature used for Boltzmann-weighting of the orientational
average energy used in u(double) and integral(double)
- setTemperature(double) - Method in class etomica.potential.P2LJQ
-
Sets the temperature used for Boltzmann-weighting of the orientational
average energy used in u(double) and integral(double)
- setTemperature(double) - Method in class etomica.potential.P2LJQQ
-
Sets the temperature used for Boltzmann-weighting of the orientational
average energy used in u(double) and integral(double)
- setTemperature(double) - Method in class etomica.potential.P2SemiclassicalAtomic
-
- setTemperature(double) - Method in class etomica.potential.P2SemiclassicalMolecular
-
- setTemperature(double) - Method in class etomica.potential.PotentialCalculationPressureTensor
-
- setTemperature(double) - Method in class etomica.statmech.MaxwellBoltzmann.Distribution
-
- setTemperature(double) - Method in class etomica.veos.VanderWaals
-
- setTemperature(double) - Method in interface etomica.virial.ClusterAbstract
-
- setTemperature(double) - Method in class etomica.virial.ClusterChainHS
-
- setTemperature(double) - Method in class etomica.virial.ClusterChainSoft
-
- setTemperature(double) - Method in class etomica.virial.ClusterCoupledFlipped
-
- setTemperature(double) - Method in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- setTemperature(double) - Method in class etomica.virial.ClusterCoupledFlippedPartial
-
- setTemperature(double) - Method in class etomica.virial.ClusterDifference
-
- setTemperature(double) - Method in class etomica.virial.ClusterExchange
-
- setTemperature(double) - Method in class etomica.virial.ClusterMultiToSingle
-
- setTemperature(double) - Method in class etomica.virial.ClusterSinglyConnected
-
- setTemperature(double) - Method in class etomica.virial.ClusterSum
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumHS
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizable
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- setTemperature(double) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- setTemperature(double) - Method in class etomica.virial.ClusterTree
-
- setTemperature(double) - Method in class etomica.virial.ClusterWeightAbs
-
- setTemperature(double) - Method in class etomica.virial.ClusterWeightSumWall
-
- setTemperature(double) - Method in class etomica.virial.ClusterWeightUmbrella
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyHS
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyMultibody
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleySoft
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleySoftBD
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
-
- setTemperature(double) - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- setTemperature(double) - Method in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- setTemperature(double) - Method in class etomica.virial.GUI.models.ModelTemperatureAndSteps
-
- setTemperature(double) - Method in class etomica.virial.MCMoveChangeBondLength
-
- setTemperature(double) - Method in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- setTemperature(double) - Method in class etomica.virial.MCMoveClusterTorsionMulti
-
- setTemperature(double) - Method in class etomica.virial.simulations.VirialH2OGCPMD.Clusterfoo
-
- setTemperatureDataSource(DataSourceUniform) - Method in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
Sets the temperature data source to the one given.
- setTemperatures(double[]) - Method in class etomica.graphics.DeviceThermoSelector
-
- setTempZSlab(int) - Method in class org.jmol.g3d.Graphics3D
-
- setTetherLength(double) - Method in class etomica.potential.P2Tether
-
Accessor method for the tether distance
- setTextBackground(Color) - Method in class etomica.graphics.DeviceBox
-
- setThermalize(IntegratorBox, double, IRandom) - Method in class etomica.modules.adsorption.P1Wall
-
- setThermostat(IntegratorMD.ThermostatType) - Method in class etomica.integrator.IntegratorMD
-
Sets the type of thermostat used by the integrator for isothermal sampling.
- setThermostatInterval(int) - Method in class etomica.integrator.IntegratorMD
-
Sets the number of integrator steps between thermostat
actions (for thermostats such as velocity scaling and Andersen).
- setThermostatNoDrift(boolean) - Method in class etomica.integrator.IntegratorMD
-
Configures the thermostat to remove any net momenta imparted
to the system after use of the thermostat.
- setTheta(double) - Method in class etomica.association.BiasVolumeSphereOriented
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.association.BiasVolumeSphereOrientedDoubleSites
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.models.water.P2HardAssociationGCPMReference
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.models.water.PNWaterGCPMThreeSite
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeReference
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeReferenceFourSites
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for angle (in radians) describing width of cone.
- setTheta(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setTheta(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setThetaFrac(double) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- setThickness(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setTHigh(double) - Method in class etomica.graphics.ColorSchemeTemperature
-
- setThreePoints(Vector, Vector, Vector) - Method in class etomica.math.geometry.Plane
-
Defines the plane by specifying three points that lie in it.
- setThreshold(double) - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.AtomFilterDeviation
-
- setThreshold(int) - Method in class etomica.graphics.DeviceDelaySlider
-
You play with fire! This allows the slider to change not increase
the activity integrate sleep period, but also to decrease the integrator
timestep.
- setTilt(double) - Method in class etomica.math.numerical.AkimaSplineSmootherApp.PlotAction
-
- setTilt(double) - Method in class etomica.math.numerical.AkimaSplineSmootherDyApp.PlotAction
-
- setTime(double) - Method in class etomica.integrator.IntegratorAnalytic.AtomTimeAction
-
- setTimeDataSource(DataSourceScalar) - Method in class etomica.data.AccumulatorHistory
-
Sets the DataSource used for the "time" component of the history.
- setTimeStep(double) - Method in class etomica.integrator.IntegratorConNVT
-
- setTimeStep(double) - Method in class etomica.integrator.IntegratorGear4
-
- setTimeStep(double) - Method in class etomica.integrator.IntegratorGear4NPH
-
- setTimeStep(double) - Method in class etomica.integrator.IntegratorMD
-
- setTimeStep(double) - Method in class etomica.integrator.IntegratorVerlet
-
- setTimeStep(double) - Method in class etomica.modules.rheology.IntegratorPolymer
-
- setTitle(String) - Method in class etomica.graphics.DeviceTable
-
Set the title of the border surrounding the table.
- setTitle(String) - Method in class etomica.graphics.DeviceToggleRadioButtons
-
- setTLow(double) - Method in class etomica.graphics.ColorSchemeTemperature
-
- setToCenter(Vector) - Method in class etomica.math.geometry.Plane
-
Sets the given vector to be the point in the plane closest to the origin.
- setToInitialPosition(int[]) - Method in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- setToInitialPosition() - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivative
-
- setToInitialPosition(int[]) - Method in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- setToInitialPosition(double[]) - Method in class etomica.models.nitrogen.FiniteDifferenceDerivativeCGNitrogenBeta
-
- setToInPlaneSquare(Vector, double, Vector[]) - Method in class etomica.math.geometry.Plane
-
Returns four points as the vertices of a square of size d centered on x0.
- setToInPlaneSquare(double, Vector[]) - Method in class etomica.math.geometry.Plane
-
inPlaneSquare with square centered on point in plane closest to origin.
- setToInPlaneVectors(Vector[]) - Method in class etomica.math.geometry.Plane
-
Computes and returns two unit vectors perpendicular to each other and in the plane.
- setTolerance(double) - Method in class etomica.action.ActionMinimizeEnergy
-
- setTolerance(double) - Method in class etomica.lattice.LatticePlane
-
- setTolerance(double) - Method in class etomica.modules.interfacial.FitTanh
-
- setTolerance(double) - Method in class etomica.surfacetension.FitTanh
-
- setTolerance(double) - Method in class etomica.virial.ClusterWheatleyMultibody
-
- setTolerance(double) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- setToNearestPoint(Vector, Vector) - Method in class etomica.math.geometry.Plane
-
Determines the point in the plane closest to the point x0 (first argument).
- setToNormalVector(Vector) - Method in class etomica.math.geometry.Plane
-
Sets the given vector to be a unit normal vector to the plane and returns it.
- setTopPadding(double) - Method in class etomica.interfacial.ConfigurationLammps
-
- setTorqueSum(PotentialCalculationTorqueSum) - Method in class etomica.integrator.IntegratorRigidIterative
-
- setTorsionpotentiala0(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setTorsionpotentiala0(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setTorsionpotentiala1(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setTorsionpotentiala1(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setTorsionpotentiala2(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setTorsionpotentiala2(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setTorsionpotentiala3(double) - Method in class etomica.virial.GUI.models.MolecularModelSKS_SpeciesAlkane
-
- setTorsionpotentiala3(double) - Method in class etomica.virial.GUI.models.MolecularModelTRAPPE_SpeciesAlkane
-
- setTotalChildren(int) - Method in class etomica.modules.sam.SpeciesAlkaneThiol
-
- setTotalChildren(int) - Method in class etomica.species.SpeciesSpheresHetero
-
Sets the total number of child atoms created by this factory.
- setTotalChildren(int) - Method in class etomica.virial.SpeciesAlkane
-
- setToU(IMoleculeList, double[]) - Method in class etomica.models.hexane.CoordinateDefinitionHexane
-
- setToU(IMoleculeList, double[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setToU(IMoleculeList, double[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- setToU(int, double, double) - Method in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- setToU(double[], Vector) - Method in class etomica.models.nitrogen.TestRotationVector
-
- setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinition
-
Set all the molecules in a cell to a position and orientation that corresponds to the
given generalized coordinate.
- setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionLeaf
-
Sets the position of the atom to be its lattice position plus the offset u
- setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionMolecule
-
- setToU(IMoleculeList, double[]) - Method in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- setToU(IMoleculeList, double[]) - Method in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- setToUMoleculei(int, double[]) - Method in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- setToUMoleculei(int, double[]) - Method in class etomica.normalmode.CoordinateDefinitionHSDimer
-
- setTracker(MCMoveTracker) - Method in class etomica.integrator.mcmove.MCMove
-
- setTransformationTensor(Tensor) - Method in class etomica.models.nitrogen.AtomActionTransformed
-
- setTransformationTensor(Tensor) - Method in class etomica.paracetamol.AtomActionTransformed
-
- setTransformFunction(IFunction) - Method in class etomica.data.AccumulatorAverageBootstrap
-
- setTranslation(Vector3f) - Method in class org.jmol.util.Matrix4f
-
Modifies the translational components of this matrix to the values of the
Vector3f argument; the other values of this matrix are not modified.
- setTranslationVector(Vector) - Method in class etomica.action.AtomActionTranslateBy
-
- setTranslucentCoverOnly(boolean) - Method in class org.jmol.g3d.Graphics3D
-
- setTransparentCursor(Object) - Method in interface org.jmol.api.ApiPlatform
-
- setTransparentCursor(Object) - Method in class org.jmol.awt.Platform
-
- setTransposed(boolean) - Method in class etomica.graphics.DisplayTable
-
If fillHorizontal is true, each data set fills a row; if false, data are
arranged to fill columns.
- setTRatio(double) - Method in class etomica.virial.MeterVirialBDBin
-
- setTRatio(double) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- setTRatio(double) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
-
- setTRatio(double) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- setTrimThreshold(float) - Method in class etomica.atom.AtomArrayList
-
- setTrimThreshold(float) - Method in class etomica.molecule.MoleculeArrayList
-
- setTrueLabel(String) - Method in class etomica.action.ActionToggle
-
Specifies the button's label when the toggle is set to true.
- setTrueLabel(String) - Method in class etomica.graphics.DeviceToggleButton
-
Specifies the button's label when the toggle is set to true.
- setTrueLabel(String) - Method in class etomica.graphics.DeviceToggleRadioButtons
-
Specifies the button's label when the toggle is set to true.
- setTruncation(double) - Method in class etomica.potential.PotentialGroupSoft
-
- setTruncationRadius(double) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2MoleculeTruncated
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncated
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncatedForceShifted
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncatedShifted
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.potential.P2SoftTruncated
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.rotation.P2LJDipole
-
Mutator method for the radial cutoff distance.
- setTruncationRadius(double) - Method in class etomica.space.BoundaryDeformablePeriodic
-
- setTSelement(ElementSimple) - Method in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- setTunable(boolean) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
Sets a flag to indicate whether tuning of the move is to be performed
Tuning adjust the step size or other property of the move with the aim of
achieving a trial acceptance rate that is near to some target value.
- setType(char) - Method in interface etomica.graph.model.Edge
-
- setType(char) - Method in class etomica.graph.model.impl.EdgeImpl
-
- setType(char) - Method in class etomica.graph.model.impl.NodeImpl
-
- setType(char) - Method in interface etomica.graph.model.Node
-
- setTypeMax(DataSourceUniform.LimitType) - Method in class etomica.data.DataSourceUniform
-
Mutator method for the type of the right limit.
- setTypeMin(DataSourceUniform.LimitType) - Method in class etomica.data.DataSourceUniform
-
Mutator method for the type of the left limit.
- setULatFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
Sets a function that returns the lattice energy for a given density.
- setULatFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeSolid
-
Sets a function that returns the lattice energy for a given density.
- setULatFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
Sets a function that returns the lattice energy for a given density.
- setULatFunction(Function) - Method in class etomica.normalmode.MeterDDP
-
Sets a function that returns the lattice energy for a given density.
- setULatFunction(Function) - Method in class etomica.normalmode.MeterDP
-
Sets a function that returns the lattice energy for a given density.
- setULatTruncFunction(Function) - Method in class etomica.normalmode.MCMoveVolumeSolid
-
Sets a function that returns the lattice energy for a given density
using the same truncation as the potentials in the system.
- setUnit(Unit) - Method in class etomica.graphics.Device
-
- setUnit(Unit) - Method in class etomica.graphics.DeviceBox
-
Accessor method to set the physical units of the displayed value.
- setUnit(Unit) - Method in class etomica.graphics.DeviceSlider
-
Override superclass setUnit method to update label when unit is changed
- setUnit(Unit) - Method in class etomica.graphics.DeviceSpinner
-
Override superclass setUnit method to update label when unit is changed
- setUnit(PrefixedUnit) - Method in class etomica.graphics.DeviceThermoSelector
-
Override superclass setUnit method to update label when unit is changed
- setUnit(Unit) - Method in class etomica.graphics.DeviceThermoSlider
-
Set the unit of temperature.
- setUnit(DataTag[], Unit) - Method in class etomica.graphics.DisplayPlot
-
- setUnit(Unit) - Method in class etomica.graphics.DisplayPlot
-
- setUnit(Unit) - Method in class etomica.graphics.DisplayScrollingGraph
-
Accessor method to set the physical units of the displayed value.
- setUnit(DataTag[], Unit) - Method in class etomica.graphics.DisplayTable
-
- setUnit(Unit) - Method in class etomica.graphics.DisplayTextBox
-
Accessor method to set the physical units of the displayed value.
- setUnit(Unit) - Method in class etomica.graphics.DisplayTextBoxesCAE
-
- setUnit(Unit) - Method in class etomica.modules.vle.DeviceThermoSliderGEMC
-
Set the unit of temperature.
- setUntransformHistograms(boolean) - Method in class etomica.data.AccumulatorAverageBootstrap
-
- setup(Box, PotentialMaster, IMoleculeList, Space) - Method in class etomica.action.CalcVibrationalModes
-
- setup() - Method in class etomica.dimer.IntegratorDimerMin
-
- setup() - Method in class etomica.dimer.IntegratorDimerRT
-
Takes in a current configuration of atoms (Rc) and creates a dimer of their positions (R1 and R2).
- setup() - Method in class etomica.dimer.IntegratorEnergyMap
-
- setup(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal
-
- setup(byte, Graph, TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal
-
- setup(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.Biconnected
-
- setup() - Method in class etomica.integrator.Integrator
-
Perform initialization.
- setup() - Method in class etomica.integrator.IntegratorManagerMC
-
- setup() - Method in class etomica.integrator.IntegratorMD
-
- setup() - Method in class etomica.kmc.IntegratorKMC
-
- setup() - Method in class etomica.kmc.IntegratorKMCCluster
-
- setup() - Method in class etomica.modules.adsorption.IntegratorHybrid
-
- setup() - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD
-
- setUp() - Method in class etomica.simulation.BenchSimDCVGCMD
-
- setUp() - Method in class etomica.simulation.BenchSimHSMD3D
-
- setUp() - Method in class etomica.simulation.BenchSimLJGCMC3D
-
- setUp() - Method in class etomica.simulation.BenchSimLJMC3D
-
- setUp() - Method in class etomica.simulation.BenchSimSurfacetensionLJMC
-
- setUp() - Method in class etomica.simulation.BenchSimSWChain
-
- setUp() - Method in class etomica.space.BenchVector3D
-
- setup() - Method in class etomica.virial.overlap.DataProcessorVirialOverlap
-
- setupActiveAtoms() - Method in class etomica.modules.adsorption.MyMCMove
-
- setupActiveAtoms() - Method in class etomica.modules.dcvgcmd.MyMCMove
-
- setupData(String, Dimension) - Method in class etomica.data.DataSourceFunction
-
Recalculates the y values from the current x values.
- setupData() - Method in class etomica.data.DataSourceRmsVelocity
-
Creates the data object (a DataFunction) to be returned by getData().
- setupData(int) - Method in class etomica.modules.chainequilibrium.MeterChainLength
-
Creates the data object (a DataFunction) to be returned by getData().
- setUpdateInterval(int) - Method in class etomica.graphics.DisplayTimer
-
Sets the period for updating the display.
- setUpdateInterval(int) - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
Sets the interval for which neighbor update checks are performed.
- setUpdateInterval(int) - Method in class etomica.nbr.list.NeighborListManager
-
Sets the interval for which neighbor update checks are performed.
- setUpdatingOnAnyChange(boolean) - Method in class etomica.data.DataSet
-
Describes protocol for firing table events that notify of column data
changes.
- setupIterators() - Method in class etomica.atom.iterator.ApiIntergroup
-
- setUpperTorsLimit(double) - Method in class etomica.models.hexane.CheckCBMCHexane
-
- setupProfileData() - Method in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- setupTargetHistogram() - Method in class etomica.virial.simulations.SimulationVirialOverlap2
-
Sets up a histogram for the target system that measures how often
maximum separation distances are visited.
- setuReactCO(double) - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- setuReactCORev(double) - Method in class etomica.modules.catalysis.ReactionManagerCO
-
- setUseNbrLists(boolean) - Method in class etomica.nbr.PotentialMasterHybrid
-
- setUseNumberLocalization(boolean) - Static method in class org.jmol.util.TextFormat
-
- setUsePermutations(boolean) - Method in class etomica.virial.ClusterBonds
-
Sets the usePermutations flag.
- setUserStylesheet(String) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Sets the user stylesheet.
- setUseSurfaceOnly(boolean) - Method in class etomica.modules.droplet.P2Cohesion
-
- setUSplitter(DataDistributer) - Method in class etomica.normalmode.DataSourceMuRoot
-
- setVA(Vector3f, float) - Method in class org.jmol.util.AxisAngle4f
-
Sets the value of this AxisAngle4f to the specified axis and angle.
- setValidate(boolean) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Defines whether or not input sources should be validated in
the conversion process
- setValue(double) - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- setValue(int) - Method in class etomica.graphics.DeviceBoxValueChangedEvent
-
Set the value of a DeviceBoxValueChangedEvent (should be the value of the text box)
- setValue(double) - Method in class etomica.graphics.DeviceSlider
-
- setValue(double) - Method in class etomica.graphics.DeviceSpinner
-
- setValue(Object) - Method in class etomica.graphics.DimensionedDoubleEditor
-
Sets the value to the given value, which is taken to be in simulation units.
- setValue(double) - Method in class etomica.graphics.DimensionedDoubleEditor
-
Sets the value to the given value, which is taken to be in simulation units.
- setValue(double) - Method in interface etomica.modifier.Modifier
-
Sets the value of the property.
- setValue(double) - Method in class etomica.modifier.ModifierFunctionWrapper
-
Applies function to given value before setting modified property.
- setValue(double) - Method in class etomica.modifier.ModifierGeneral
-
- setValue(double) - Method in class etomica.modifier.ModifierNMolecule
-
- setValue(double) - Method in class etomica.modules.adsorption.ModifierPMu
-
- setValue(double) - Method in class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
-
- setValue(double) - Method in class etomica.modules.crystalviewer.LatticeEditor.NModifier
-
- setValue(double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu1Modulator
-
- setValue(double) - Method in class etomica.modules.dcvgcmd.IntegratorDCVGCMD.Mu2Modulator
-
- setValue(double) - Method in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- setValue(double) - Method in class etomica.modules.entropylottery.ModifierDimensions
-
- setValue(double) - Method in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- setValue(double) - Method in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- setValue(double) - Method in class etomica.modules.mu.MuGraphic.ModifierEpsilon
-
- setValue(double) - Method in class etomica.modules.mu.MuGraphic.ModifierLambda
-
- setValue(double) - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
-
- setValue(double) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
-
- setValue(double) - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierPistonDensity
-
- setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierEpsilon
-
- setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierEpsilon
-
- setValue(double) - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierSoluteCharge
-
- setValue(double) - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
-
- setValue(double) - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
-
- setValue(double) - Method in class etomica.normalmode.ModifierCells3D
-
- setValue(double) - Method in class etomica.normalmode.ModifierXCells2D
-
- setValue(double) - Method in class etomica.normalmode.ModifierYCells2D
-
- setValue(Field, String) - Method in class etomica.util.ParameterBase
-
- setValue(Object, Field, String) - Method in interface etomica.util.ParameterParser
-
Sets obj's field to appropriate value based on the given string, if this
parser is appropriate for the given field, or throws an exception if
it's not.
- setValue(double) - Method in class etomica.virial.simulations.ModifierTPI
-
- setValueAt(Object, int, int) - Method in class etomica.graphics.DeviceTableModelGeneric
-
Set the value in the given table cell.
- setValueAt(Object, int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable
-
- setValueAt(Object, int, int) - Method in class etomica.virial.GUI.models.ModelMoleculeListDisplayTable_new
-
- setValueAt(Object, int, int) - Method in class etomica.virial.GUI.models.ModelPotParamDisplayTable
-
- setValueForAction(double) - Method in class etomica.modifier.ModifyAction
-
Stores the new value to be set by the wrapped modifier.
- setValueForAction(boolean) - Method in class etomica.modifier.ModifyBooleanAction
-
Stores the new value to be set by the wrapped modifier.
- setVaporColor(Color) - Method in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- setVariable(String, Set<Graph>) - Method in interface etomica.graph.engine.Environment
-
- setVariable(String, Set<Graph>) - Method in class etomica.graph.engine.impl.EnvironmentImpl
-
- setVCut(double) - Method in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
-
- setVCut(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
-
- setVectorScale(Vector) - Method in class etomica.action.BoxInflate
-
Sets the scale defining the amount of inflation for each dimension.
- setVertex1(Vector) - Method in class etomica.math.geometry.LineSegment
-
- setVertex2(Vector) - Method in class etomica.math.geometry.LineSegment
-
- setVFunc(PotentialCalculationMappedVirialV.VFunc) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- setViewSpeciesSelection(ViewSpeciesSelection) - Method in class etomica.virial.GUI.views.AppViewMixtureBuilder
-
- setVisible(boolean) - Method in class etomica.graph.viewer.ClusterViewer
-
- setVisible(boolean) - Method in class etomica.graphics.AboutBoxWindow
-
- setVMax(double) - Method in class etomica.graphics.DisplayScrollingGraph
-
- setVMin(double) - Method in class etomica.graphics.DisplayScrollingGraph
-
- setVolFluctuation(boolean) - Method in class etomica.models.nitrogen.MeterNormalizedCoord
-
- setVolume(double) - Method in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
Sets volume to an arbitrary value (instead of the box volume).
- setVolume(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
Sets volume to an arbitrary value (instead of the box volume).
- setVolume(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
Sets volume to an arbitrary value (instead of the box volume).
- setVolume(double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
Sets volume to an arbitrary value (instead of the box volume).
- setVolumeBias(IFunction) - Method in class etomica.integrator.mcmove.MCMoveVolume
-
- setVZero(double) - Method in class etomica.yukawa.P2Yukawa
-
- setW(double) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- setWallDim(int) - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
- setWallDim(int) - Method in class etomica.modules.sam.P1WCAWall
-
- setWallDim(int) - Method in class etomica.nbr.CriterionPositionWall
-
Sets the orientation of the wall to be perpendicular to the given dimension
- setWallPosition(double) - Method in class etomica.modules.sam.P1WCAWall
-
- setWallPosition(double) - Method in class etomica.nbr.CriterionPositionWall
-
Sets the position of the wall.
- setWallPosition(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setWallVelocity(double) - Method in class etomica.potential.P1HardMovingBoundary
-
- setWaveVec(Vector[]) - Method in class etomica.data.meter.MeterStructureFactor
-
- setWaveVector(Vector) - Method in class etomica.normalmode.MeterHarmonicCoordinate
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setWaveVectorCoefficients(double[]) - Method in class etomica.normalmode.MCMoveSingleMode
-
- setWaveVectorFactory(WaveVectorFactory) - Method in class etomica.normalmode.CalcJacobian
-
Sets the object that defines the normal-coordinate wave vectors.
- setWaveVectorFactory(WaveVectorFactory) - Method in class etomica.normalmode.MeterNormalMode
-
Sets the object that defines the normal-coordinate wave vectors.
- setWaveVectorFactory(WaveVectorFactory) - Method in class etomica.normalmode.WriteS
-
- setWaveVectorNum(int) - Method in class etomica.normalmode.DeviceWaveVectorSlider
-
Set the current value for the wavevector # slider/text box.
- setWaveVectorNum(int) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setWaveVectors(Vector[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
Set the wave vectors used by the move.
- setWaveVectors(Vector[]) - Method in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
Set the wave vectors that can be changed by the move.
- setWaveVectors(Vector[]) - Method in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
Set the wave vectors accessible to the move.
- setWaveVectors(Vector[]) - Method in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- setWaveVectors(Vector[]) - Method in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- setWaveVectors(Vector[]) - Method in class etomica.models.oneDHardRods.MeterF
-
- setWaveVectors(Vector[]) - Method in class etomica.models.oneDHardRods.MeterWidomMode
-
- setWaveVectors(Vector[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- setWaveVectors(Vector[]) - Method in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- setWaveVectors(Vector[]) - Method in class etomica.normalmode.IntegratorHarmonic
-
- setWaveVectors(Vector[]) - Method in class etomica.normalmode.MCMoveHarmonic
-
- setWaveVectors(Vector[]) - Method in class etomica.normalmode.MCMoveSingleMode
-
Set the wave vectors used by the move.
- setWaveVectors(Vector[], double[]) - Method in class etomica.normalmode.MeterHarmonicEnergy
-
- setWaveVectors(Vector[], double[]) - Method in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- setWeight(Rational) - Method in class etomica.virial.cluster.ClusterDiagram
-
- setWeight(double) - Method in class etomica.virial.MeterVirialBDBin
-
- setWeight(double) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- setWeight(double) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- setWeight(double) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- setWeightCoefficients(double[]) - Method in class etomica.virial.ClusterWeightUmbrella
-
- setWeightUpdateInterval(int) - Method in class etomica.tmmc.IntegratorTMMC
-
Sets the number of doStep calls between updating of weights.
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for attractive-well diameter divided by sigma;
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for attractive-well diameter divided by sigma;
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for attractive-well diameter divided by sigma;
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for attractive-well diameter divided by sigma;
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for attractive-well diameter divided by sigma;
- setWellCutoffFactor(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for attractive-well diameter divided by sigma;
- setWellDiameter(double) - Method in class etomica.potential.P2HardAssociation
-
Accessor for well-diameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationCone
-
Accessor method for attractive-well depth parameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
Accessor method for attractive-well depth parameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
Accessor method for attractive-well depth parameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeFourSitesSW
-
Accessor method for attractive-well depth parameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
Accessor method for attractive-well depth parameter.
- setWellEpsilon(double) - Method in class etomica.potential.P2HardAssociationConeSW
-
Accessor method for attractive-well depth parameter.
- setWidth(float) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
In less than or equal to zero, the width is not
constrained on the output image.
- setWidthHeight(boolean) - Method in class org.jmol.util.GData
-
- setWindow(double, double, double, double) - Method in class etomica.modules.clustergenerator.Plot
-
Sets up a mapping from physical units to pixel units.
- setWindowParameters(int, int, boolean) - Method in class org.jmol.g3d.Graphics3D
-
- setWindowParameters(int, int, boolean) - Method in class org.jmol.util.GData
-
- setWireFrame(boolean) - Method in class g3dsys.images.ImageShell
-
- setWithReplacement(boolean) - Method in class etomica.data.AccumulatorAverageBootstrap
-
- setWrappedPotential(PotentialHard) - Method in class etomica.potential.P2HardWrapper
-
- setWrappedPotential(IPotentialAtomic) - Method in class etomica.potential.P2MoleculeMonatomic
-
- setWriteInterval(int) - Method in class etomica.data.DataLogger
-
Define how many number of interval events received between writings to
file.
- setWriteInterval(int) - Method in class etomica.zeolite.MSDCoordWriter
-
Equates intervalAction method variable to variable passed in from simulation class
- setWriteOnFinish(IDataSource) - Method in class etomica.data.DataLogger
-
- setWriteOnInterval(boolean) - Method in class etomica.data.DataLogger
-
- setWriteScale(boolean) - Method in class etomica.graphics.DisplayCanvas
-
- setWriteVelocity(boolean) - Method in class etomica.action.WriteConfigurationDLPOLY
-
- setWriteVelocity(boolean) - Method in class etomica.action.WriteConfigurationP2DLPOLY
-
- setX(double, double, int) - Method in class etomica.data.meter.MeterPressureByVolumeChange
-
- setX(int, double) - Method in interface etomica.space.Vector
-
Sets the i-th component of the vector to the given value d.
- setX(int, double) - Method in class etomica.space1d.Vector1D
-
- setX(int, double) - Method in class etomica.space2d.Vector2D
-
- setX(int, double) - Method in class etomica.space3d.Vector3D
-
- setX(int, double) - Method in class etomica.spaceNd.VectorND
-
- setX(float) - Method in class g3dsys.images.Ball
-
set the x molspace position of the figure
- setX(float) - Method in class g3dsys.images.Ellipse
-
set the x molspace position of the figure
- setX0(Vector) - Method in class etomica.potential.P1Harmonic
-
- setXCellModifier(Modifier) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the x-Cell # modifier object.
- setXCellNum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the current value for the xCell # slider/text box.
- setXComp() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the "x-axis" button to its selected state.
- setXDataSource(DataSourceIndependent) - Method in class etomica.data.types.DataFunction.DataInfoFunctionFactory
-
Sets array of independent DataInfo.
- setXFlipped(boolean) - Method in class g3dsys.control.G3DSys
-
- setXLabel(String) - Method in class etomica.graphics.DisplayPlot
-
- setXMax(double) - Method in class etomica.data.DataSourceUniform
-
Mutator method for the right limit of the range.
- setXMin(double) - Method in class etomica.data.DataSourceUniform
-
Mutator method for the left limit of the range.
- setXRange(DoubleRange) - Method in interface etomica.data.histogram.Histogram
-
Sets the range of x values used in the histogram (min and max).
- setXRange(DoubleRange) - Method in class etomica.data.histogram.HistogramCollapsing
-
- setXRange(DoubleRange) - Method in class etomica.data.histogram.HistogramDiscrete
-
- setXRange(DoubleRange) - Method in class etomica.data.histogram.HistogramExpanding
-
- setXRange(DoubleRange) - Method in class etomica.data.histogram.HistogramNotSoSimple
-
- setXRange(DoubleRange) - Method in class etomica.data.histogram.HistogramReweightedData
-
- setXRange(DoubleRange) - Method in class etomica.data.histogram.HistogramSimple
-
- setXRange(double, double, int) - Method in class etomica.integrator.mcmove.MCMoveAtomInRegion
-
Defines the region atoms must be selected from.
- setXRot(float) - Method in class etomica.graphics.DisplayCanvas
-
- setXScale(double, double, double) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the minimum and maximum X-axis limits on the function display
sliders.
- setXSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the post slider value changed action.
- setXUnit(Unit) - Method in class etomica.graphics.DisplayPlot
-
Extend superclass method to update label with change of unit.
- setXYZChange() - Method in class etomica.models.nitrogen.MCMoveVolumeN2
-
- setY(float) - Method in class g3dsys.images.Ball
-
set the y molspace position of the figure
- setY(float) - Method in class g3dsys.images.Ellipse
-
set the y molspace position of the figure
- setYCellModifier(Modifier) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the y-Cell # modifier object.
- setYCellNum(int) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the current value for the yCell # slider/text box.
- setYComp() - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
Set the "y-axis" button to its selected state.
- setYesButton(JButton) - Method in class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
-
- setYFlipped(boolean) - Method in class g3dsys.control.G3DSys
-
- setYRot(float) - Method in class etomica.graphics.DisplayCanvas
-
- setYScale(double, double, double) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the minimum and maximum Y-axis limits on the function display
sliders.
- setYScale(double) - Method in class etomica.modules.entropylottery.DisplayBoxCanvas1DBins
-
- setYSliderPostAction(IAction) - Method in class etomica.normalmode.DeviceCellNumXYSlider
-
- setZ(double) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- setZ(float) - Method in class g3dsys.images.Ball
-
set the z molspace position of the figure
- setZ(float) - Method in class g3dsys.images.Ellipse
-
set the z molspace position of the figure
- setZ1(double) - Method in class etomica.potential.P2ModifiedMorse
-
- setZ2(double) - Method in class etomica.potential.P2ModifiedMorse
-
- setZ3() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setZ4211() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setZ4220() - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- setZero() - Method in class org.jmol.util.Matrix3f
-
Sets this matrix to all zeros.
- setZero() - Method in class org.jmol.util.Matrix4f
-
Sets this matrix to all zeros.
- setZeroForce(boolean) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- setZFraction(double, double) - Method in class etomica.modules.adsorption.MyMCMove
-
Sets the zFraction, the fraction of the box volume into which atoms are
inserted or deleted.
- setZFraction(double) - Method in class etomica.modules.dcvgcmd.MyMCMove
-
Sets the zFraction, the fraction of the box volume into which atoms are
inserted or deleted.
- setZoom(float) - Method in class etomica.graphics.DisplayCanvas
-
- setZShade(boolean, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- setZShade(boolean, int, int, int) - Method in class org.jmol.util.GData
-
- sfacData - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- sfacDataInfo - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- sfacPlotSink - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ModifierConfiguration
-
- shadeIndexLast - Static variable in class org.jmol.util.Shader
-
- shadeIndexMax - Static variable in class org.jmol.util.Shader
-
- shadeIndexNoisyLimit - Static variable in class org.jmol.util.Shader
-
- shadeIndexNormal - Static variable in class org.jmol.util.Shader
-
- Shader - Class in org.jmol.util
-
All static functions.
- Shader() - Constructor for class org.jmol.util.Shader
-
- shakeAgentManager - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- shakeTol - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- Shape - Interface in etomica.math.geometry
-
Interface for an object that defines a closed region of space.
- shape - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
-
- shape - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
-
- shape - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
-
- shape - Variable in class etomica.space.Boundary
-
- shape - Variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- shape - Static variable in class org.jmol.script.Token
-
- SHAPE_AXES - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_BACKBONE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_BALLS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_BBCAGE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_CARTOON - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_CONTACT - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_DIPOLES - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_DOTS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_DRAW - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_ECHO - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_ELLIPSOIDS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_FRANK - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_GEOSURFACE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_HALOS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_HOVER - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_HSTICKS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_ISOSURFACE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_LABELS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_LCAOCARTOON - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_HAS_ID - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_MESH_COLLECTION - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_SECONDARY - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_SIZE_ZERO_ON_RESTRICT - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_SPECIAL - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MAX_SURFACE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MEASURES - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MESHRIBBON - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MIN_HAS_ID - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MIN_MESH_COLLECTION - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MIN_SECONDARY - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MIN_SPECIAL - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MIN_SURFACE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_MO - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_PLOT3D - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_PMESH - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_POLYHEDRA - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_RIBBONS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_ROCKETS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_SSSTICKS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_STARS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_STICKS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_STRANDS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_STRUTS - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_TRACE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_UCCAGE - Static variable in class org.jmol.viewer.JmolConstants
-
- SHAPE_VECTORS - Static variable in class org.jmol.viewer.JmolConstants
-
- shapeClassBases - Static variable in class org.jmol.viewer.JmolConstants
-
- ShapeData() - Constructor for class etomica.virial.simulations.ShapeParser.ShapeData
-
- ShapeParser - Class in etomica.virial.simulations
-
- ShapeParser() - Constructor for class etomica.virial.simulations.ShapeParser
-
- ShapeParser.ShapeData - Class in etomica.virial.simulations
-
- shapes - Variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- shapeTokenIndex(int) - Static method in class org.jmol.viewer.JmolConstants
-
- shareData - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- shareData - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- shearBox - Variable in class etomica.modules.rheology.RheologyGraphic
-
- shearRate - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- sheet - Static variable in class org.jmol.script.Token
-
- sheetsmoothing - Static variable in class org.jmol.script.Token
-
- shift - Variable in class etomica.interfacial.ConfigurationLammps
-
- shift - Variable in class etomica.interfacial.WriteConfigurationInterfacial
-
- shift - Variable in class etomica.metastable.MeterDensityDistribution
-
- shift - Variable in class etomica.models.co2.PNCO2GCPM
-
- shift - Variable in class etomica.models.co2.PNGCPM
-
- shift - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- shift - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- shift - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- shift - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- shift - Variable in class etomica.models.water.P2Water3P
-
- shift - Variable in class etomica.models.water.P2Water4P
-
- shift - Variable in class etomica.models.water.PNWaterGCPM
-
- shift(int) - Method in class etomica.modules.render.ParseObj.BondInfo
-
- shift - Variable in class etomica.potential.P2CO2EMP
-
- shift - Variable in class etomica.potential.P2SoftSphericalTruncatedShifted
-
- shift - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
-
- shift0 - Variable in class etomica.space.BoundaryRectangular
-
- shift0 - Variable in class etomica.space3d.BoundaryTruncatedOctahedron
-
- shifted - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- shiftMomenta() - Method in class etomica.integrator.IntegratorMD
-
Subtracts velocity from all atoms such that the new net momentum of
the whole system is zero.
- shiftMomenta() - Method in class etomica.integrator.IntegratorRigidIterative
-
- shiftMomenta() - Method in class etomica.integrator.IntegratorRigidMatrixIterative
-
- shiftMomenta() - Method in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- showaxes - Static variable in class org.jmol.script.Token
-
- showBoundary - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- showboundbox - Static variable in class org.jmol.script.Token
-
- showfrank - Static variable in class org.jmol.script.Token
-
- showhiddenselectionhalos - Static variable in class org.jmol.script.Token
-
- showhydrogens - Static variable in class org.jmol.script.Token
-
- showingColumnHeaders - Variable in class etomica.graphics.DisplayTable
-
- showingRowLabels - Variable in class etomica.graphics.DisplayTable
-
- showingUnits - Variable in class etomica.graphics.DisplayTable
-
- showkeystrokes - Static variable in class org.jmol.script.Token
-
- showmeasurements - Static variable in class org.jmol.script.Token
-
- showmultiplebonds - Static variable in class org.jmol.script.Token
-
- shownavigationpointalways - Static variable in class org.jmol.script.Token
-
- showNumMoleculesPlots - Variable in class etomica.modules.vle.VLE
-
- showPlane - Variable in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- showPointInput(boolean) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the visibility of the data point input table.
- showReport(SimulationVirialOverlap2, IntegratorListener) - Method in class etomica.virial.GUI.components.SimulationRunner
-
- showScale(boolean) - Method in class etomica.graphics.DevicePlotPoints
-
Sets the visibility of the plot axis limit sliders.
- showscript - Static variable in class org.jmol.script.Token
-
- ShowStep - Class in etomica.models.hexane
-
- ShowStep() - Constructor for class etomica.models.hexane.ShowStep
-
- showtiming - Static variable in class org.jmol.script.Token
-
- showunitcell - Static variable in class org.jmol.script.Token
-
- sidechain - Static variable in class org.jmol.script.Token
-
- sig - Variable in class etomica.virial.ClusterWheatleyHS.AllSigs
-
- sig - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- sig2 - Variable in class etomica.graphics.ColorSchemeOverlap
-
- sig2 - Variable in class etomica.potential.P2HardSphere
-
Square of collisionDiameter
- sigBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- sigBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- sigBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- sigBox - Variable in class etomica.modules.swmd.SwmdGraphic
-
- sigCounter - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- sigma - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
-
- sigma - Variable in class etomica.models.water.P2Water3P
-
- sigma - Variable in class etomica.models.water.P2Water4P
-
- SIGMA - Static variable in class etomica.models.water.P2WaterSPCE
-
- sigma - Variable in class etomica.models.water.P2WaterTIP4PHardCore
-
- sigma - Variable in class etomica.models.water.PNWaterGCPM
-
- sigma - Variable in class etomica.modules.adsorption.EOSSW
-
- sigma - Variable in class etomica.modules.adsorption.P1Wall
-
- sigma - Variable in class etomica.modules.colloid.P1Wall
-
- sigma - Variable in class etomica.modules.dcvgcmd.P1WCAWall
-
- sigma - Variable in class etomica.modules.droplet.DropletAtomic
-
- sigma - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- sigma - Variable in class etomica.modules.sam.P1WCAWall
-
- sigma - Variable in class etomica.modules.swmd.SwmdGraphic
-
- sigma - Variable in class etomica.modules.vle.VLESim
-
- sigma - Variable in class etomica.normalmode.SoftSphereSolidEOS
-
- sigma - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- sigma - Variable in class etomica.potential.P1HardPeriodic
-
- sigma - Variable in class etomica.potential.P2ElectrostaticWithHardCore
-
- sigma(double) - Method in class etomica.potential.P3HydrogenManzhos
-
- sigma - Variable in class etomica.units.systems.LJ
-
- sigma(int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate sigma(n).
- sigma(BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate sigma(n).
- sigma() - Method in class etomica.veos.bigdecimal.Ifactor
-
Sum of the divisors of the number.
- sigma(int) - Method in class etomica.veos.bigdecimal.Ifactor
-
Sum of the k-th powers of divisors of the number.
- sigma - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
-
- sigma - Variable in class etomica.virial.MCMoveClusterAtomChainHSTail
-
- sigma - Variable in class etomica.virial.MCMoveClusterAtomHSChain
-
- sigma - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- sigma - Variable in class etomica.virial.MCMoveClusterAtomHSTree
-
- sigma - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
-
- sigma - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
-
- sigma - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
-
- sigma - Variable in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
-
- sigma0point - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigma0point - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- sigma0point - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- sigma0point - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigma2 - Variable in class etomica.models.water.P2Water3P
-
- sigma2 - Variable in class etomica.models.water.P2Water4P
-
- sigma2 - Variable in class etomica.models.water.P2WaterTIP4PHardCore
-
- sigma2 - Variable in class etomica.modules.sam.P1WCAWall
-
- sigma2 - Variable in class etomica.normalmode.HSNPT.HSMD3DParameters
-
- sigma2 - Variable in class etomica.virial.MayerHSMixture
-
- sigma2 - Variable in class etomica.virial.MayerWell
-
- sigmaA - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- sigmaABpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaABpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- sigmaABpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- sigmaABpoint - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaAll - Variable in class etomica.models.co2.PNCO2GCPM
-
- sigmaApoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaApoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- sigmaApoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- sigmaApoint - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaBpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaBpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- sigmaBpoint - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- sigmaBpoint - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaC - Variable in class etomica.models.co2.PNCO2GCPM
-
- sigmaC - Variable in class etomica.potential.P2CO2EMP
-
- sigmaC2 - Variable in class etomica.potential.P2CO2EMP
-
- sigmaCH2 - Variable in class etomica.modules.sam.Sam
-
- sigmaCH2 - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- sigmaCH2 - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- sigmaCH2 - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- sigmaCH2 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- sigmaCH3 - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- sigmaCH3 - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- sigmaCH3 - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- sigmaCH3 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- sigmaCO - Variable in class etomica.potential.P2CO2EMP
-
- sigmaCO2 - Variable in class etomica.potential.P2CO2EMP
-
- sigmaColloid - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- sigmaH - Variable in class etomica.models.water.PNWaterGCPM
-
- sigmaHC - Static variable in class etomica.potential.P2HePCKLJS
-
- sigmaHC2 - Variable in class etomica.potential.P2HeSimplified
-
- sigmaHS - Variable in class etomica.AlkaneEH.DHS_NVT.Param
-
- sigmaHS - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
-
- sigmaHS - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
-
- sigmaHS2 - Variable in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.P2WaterDHS
-
- sigmaHSRef - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
-
- sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.ReeHooverMC.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAceticAcid.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialB3C1TIP4Pwater.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialB3C2TIP4Pwater.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2OGCPMD.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJBridge.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJD.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialSW.VirialSWParam
-
- sigmaHSRef - Variable in class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
-
- sigmak(BigInteger, int) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate sigma_k(n).
- sigmaLJ - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- sigmaLJ - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- sigmaLJ - Variable in class etomica.dielectric.TIP4P_NVT
-
- sigmaM - Variable in class etomica.models.water.PNWaterGCPM
-
- sigmaMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- sigmaMonomer - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- sigmaN - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- sigmaO - Variable in class etomica.models.co2.PNCO2GCPM
-
- sigmaO - Variable in class etomica.potential.P2CO2EMP
-
- sigmaO2 - Variable in class etomica.potential.P2CO2EMP
-
- sigmaOC - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- sigmaOH - Static variable in class etomica.virial.simulations.VirialRowleyAlcohol
-
- sigmaSF6 - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- sigmaSolute - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- sigmaSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- signature() - Method in class etomica.atom.Atom
-
Returns a string of digits that uniquely identifies this atom.
- signature() - Method in class etomica.molecule.Molecule
-
Returns a string of digits that uniquely identifies this atom.
- signature() - Method in class etomica.units.dimensions.Dimension
-
The signature is the exponents of each of the base dimensions forming the
given dimension.
- signatureMaker - Variable in class etomica.graph.iterators.filters.GlobalFilter
-
- SignatureMaker() - Constructor for class etomica.graph.iterators.filters.GlobalFilter.SignatureMaker
-
- signum() - Method in class etomica.veos.bigdecimal.BigSurd
-
The sign: 1 if the number is >0, 0 if ==0, -1 if <0
- signum() - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Sign function.
- signum() - Method in class etomica.veos.bigdecimal.Rational
-
The sign: 1 if the number is >0, 0 if ==0, -1 if <0
- Silver - Class in etomica.chem.elements
-
Class for the Silver element.
- Silver(String) - Constructor for class etomica.chem.elements.Silver
-
- Silver(String, double) - Constructor for class etomica.chem.elements.Silver
-
- SILVER - Static variable in class org.jmol.util.Colix
-
- sim - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- sim - Variable in class etomica.atom.AtomTypeAgentManager
-
- sim - Variable in class etomica.box.BoxAgentSourceMoleculeManager
-
- sim - Variable in class etomica.data.meter.MeterKineticEnergyRigid
-
- sim - Variable in class etomica.data.meter.MeterTemperature
-
- sim - Variable in class etomica.dimer.IntegratorDimerMin
-
- sim - Variable in class etomica.dimer.IntegratorDimerRT
-
- sim - Variable in class etomica.graphics.DisplayBox
-
- sim - Variable in class etomica.integrator.IntegratorRigidIterative
-
- sim - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- sim - Variable in class etomica.modules.adsorption.AdsorptionGraphic
-
- sim - Variable in class etomica.modules.catalysis.CatalysisGraphic
-
- sim - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- sim - Variable in class etomica.modules.catalysis.ReactionManagerCO
-
- sim - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
-
- sim - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
-
- sim - Variable in class etomica.modules.colloid.ColloidGraphic
-
- sim - Variable in class etomica.modules.crystalviewer.CrystalViewer
-
- sim - Variable in class etomica.modules.droplet.DropletAtomicGraphic
-
- sim - Variable in class etomica.modules.droplet.DropletGraphic
-
- sim - Variable in class etomica.modules.ensembles.LJMCGraphic
-
- sim - Variable in class etomica.modules.entropylottery.EntropyLotteryGraphic
-
- sim - Variable in class etomica.modules.insertion.InsertionGraphic
-
- sim - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- sim - Variable in class etomica.modules.ljmd.LjmdGraphic
-
- sim - Variable in class etomica.modules.mu.MuGraphic
-
- sim - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicGraphicMC
-
- sim - Variable in class etomica.modules.multiharmonic.MultiharmonicGraphic
-
- sim - Variable in class etomica.modules.multiharmonic.MultiharmonicGraphicMC
-
- sim - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- sim - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicGraphicMC
-
- sim - Variable in class etomica.modules.osmosis.Osmosis
-
- sim - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibriumGraphic
-
- sim - Variable in class etomica.modules.render.RenderMDGraphic
-
- sim - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- sim - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- sim - Variable in class etomica.modules.rosmosis.MeterFlux
-
- sim - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- sim - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- sim - Variable in class etomica.modules.sam.ConfigurationSAM
-
- sim - Variable in class etomica.modules.sam.CriterionTether3
-
- sim - Variable in class etomica.modules.sam.SamGraphic.DataPipeStressStrain
-
- sim - Variable in class etomica.modules.statistics.StatisticsMCGraphic
-
- sim - Variable in class etomica.modules.swmd.SwmdGraphic
-
- sim - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- sim - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- sim - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- sim - Variable in class etomica.nbr.cell.NeighborCellManager
-
- sim - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
-
- sim - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- sim - Variable in class etomica.normalmode.HTTPSoftSphereApplet
-
- sim - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- sim - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- sim - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- sim - Variable in class etomica.normalmode.nptdemo.HSNPT2DGraphic
-
- sim - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- sim - Variable in class etomica.threaded.domain.BoxAgentSourceCellManagerThreaded
-
- SIM - Static variable in class etomica.units.systems.UnitSystem
-
Instance of simulation units, the unit system used for internal calculations.
- Sim() - Constructor for class etomica.units.systems.UnitSystem.Sim
-
- SIM_CONTEXT_CLASSES - Static variable in class etomica.server.core.construction.Construction
-
- SIM_UNIT - Static variable in class etomica.units.dimensions.Angle
-
- SIM_UNIT - Static variable in class etomica.units.dimensions.Area
-
- SIM_UNIT - Static variable in class etomica.units.dimensions.Charge
-
Simulation unit of charge.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Current
-
Simulation unit of electrical current.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Dipole
-
- SIM_UNIT - Static variable in class etomica.units.dimensions.ElectricPotential
-
Simulation unit of charge.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Energy
-
The simulation unit of energy is D-A^2/ps^2.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Force
-
- SIM_UNIT - Static variable in class etomica.units.dimensions.Fraction
-
The simulation unit is the Decimal.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Frequency
-
The simulation unit is 1/ps = 1/(10^-12 s) = 10^12/s = 1 THz.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Length
-
Simulation unit for length is the angstrom.
- SIM_UNIT - Static variable in class etomica.units.dimensions.LuminousIntensity
-
The Candela unit.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Mass
-
The simulation unit is the Dalton.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Momentum
-
The simulation unit is A/ps.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Power
-
The simulation unit of power is D-A^2/ps^3.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Pressure
-
Simulation unit of pressure is (D-A/ps^2)/A^2 = D/(A-ps^2).
- SIM_UNIT - Static variable in class etomica.units.dimensions.Pressure2D
-
- SIM_UNIT - Static variable in class etomica.units.dimensions.Quantity
-
Simulation unit is Count.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Temperature
-
The simulation unit for temperature, which as kT has dimensions
of energy and is D-A^2/ps^2.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Time
-
Simulation unit for time is the picosecond.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Velocity
-
The simulation unit is A/ps.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Viscosity
-
The simulation unit is Dalton/(A-ps).
- SIM_UNIT - Static variable in class etomica.units.dimensions.Volume
-
Simulation unit of volume is cubic Angstroms.
- SIM_UNIT - Static variable in class etomica.units.dimensions.Wavenumber
-
The simulation unit is 1/A
- SimBennet - Class in etomica.normalmode
-
Simulation to sample Bennet's Overlap Region
- SimBennet(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimBennet
-
- SimBennet.SimBennetParam - Class in etomica.normalmode
-
- SimBennetParam() - Constructor for class etomica.normalmode.SimBennet.SimBennetParam
-
- SimBennetParam() - Constructor for class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
-
- SimBennetParam() - Constructor for class etomica.normalmode.SimTargetUmbrella.SimBennetParam
-
- SimBennetParam() - Constructor for class etomica.normalmode.SimUmbrella.SimBennetParam
-
- SimBennetParam() - Constructor for class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
-
- SimCalcJ - Class in etomica.normalmode
-
Simulation class of hard spheres in 1D or 3D that calculates the dq/dx
Jacobian.
- SimCalcJ(Space, int) - Constructor for class etomica.normalmode.SimCalcJ
-
- SimCalcS - Class in etomica.normalmode
-
MD simulation of hard spheres in 1D or 3D with tabulation of the
collective-coordinate S-matrix.
- SimCalcS(Space, int, double) - Constructor for class etomica.normalmode.SimCalcS
-
- SIMCALCS - Static variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- SIMCALCS - Static variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- SimCalcSLJ - Class in etomica.normalmode
-
MD simulation of hard spheres in 1D or 3D with tabulation of the
collective-coordinate S-matrix.
- SimCalcSLJ(Space, int, double, double) - Constructor for class etomica.normalmode.SimCalcSLJ
-
- SimCalcSMorse - Class in etomica.normalmode
-
MC simulation of Morse model in 3D with tabulation of the
collective-coordinate S-matrix.
- SimCalcSMorse(Space, int, double, double) - Constructor for class etomica.normalmode.SimCalcSMorse
-
- SimCalcSSoftSphere2D - Class in etomica.normalmode
-
MC simulation of FCC soft-sphere model in 2D with tabulation of the
collective-coordinate S-matrix.
- SimCalcSSoftSphere2D(Space, int, int[], double, int) - Constructor for class etomica.normalmode.SimCalcSSoftSphere2D
-
- SimCalcSSoftSphereFCC - Class in etomica.normalmode
-
MC simulation of FCC soft-sphere model in 3D with tabulation of the
collective-coordinate S-matrix.
- SimCalcSSoftSphereFCC(Space, int, double, double, int) - Constructor for class etomica.normalmode.SimCalcSSoftSphereFCC
-
- SimCalcSSoftSphereFCCSuperBox - Class in etomica.normalmode
-
MC simulation of FCC soft-sphere model in 3D with tabulation of the
collective-coordinate S-matrix.
- SimCalcSSoftSphereFCCSuperBox(Space, int, double, double, int) - Constructor for class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- simCDef - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simCDef - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- simCDim - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simCDim - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- SimClassInfo - Class in etomica.server.representations
-
- SimClassInfo(String, String) - Constructor for class etomica.server.representations.SimClassInfo
-
- SimDegFreeBinning - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Output: histogram files of probability that a mode is zero
Calculate free energy of solid
Treats modes as degrees of freedom
- SimDegFreeBinning(Space, int, double, int, int) - Constructor for class etomica.models.oneDHardRods.SimDegFreeBinning
-
- SimDegFreeBinning.SimParam - Class in etomica.models.oneDHardRods
-
- SimDegreeFreedom - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Output: histogram files of probability that a mode is zero
Calculate free energy of solid
Treats modes as degrees of freedom
- SimDegreeFreedom(Space, int, double, int, int) - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom
-
- SimDegreeFreedom.SimParam - Class in etomica.models.oneDHardRods
-
- SimDegreeFreedom3D - Class in etomica.models.oneDHardRods
-
MC simulation
3D hard spheres
No graphic display
Output: histogram files of probability that a mode is zero
Calculate free energy of solid
Treats modes as degrees of freedom
- SimDegreeFreedom3D(Space, int, double, int, int, String) - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom3D
-
- SimDegreeFreedom3D.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImage - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Calculate free energy of solid
Treats modes as degrees of freedom; keeps one rod at each end that does not
move by central image.
- SimDifferentImage(Space, int, double, int, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImage
-
- SimDifferentImage.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImage1D - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Calculate free energy of solid
Treats modes as degrees of freedom; keeps one rod at each end that does not
move by central image.
- SimDifferentImage1D(Space, int, double, int, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1D
-
- SimDifferentImage1D.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImage1DHR - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Calculate free energy of solid
Treats modes as degrees of freedom; keeps one rod at each end that does not
move by central image.
- SimDifferentImage1DHR(Space, int, double, int, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1DHR
-
- SimDifferentImage1DHR.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImageSsFcc - Class in etomica.models.oneDHardRods
-
MC simulation
3D Lennard Jones
FCC crystal
No graphic display
Uses wavevector approach
Calculate free energy of solid using normal mode insertion method
Treats coupling of modes as overlap variable;
Generate input files with HarmonicCrystalSoftSphereFCC
Uses overlap sampling.
- SimDifferentImageSsFcc(Space, int[], int[], double, int, double, int, String, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFcc
-
- SimDifferentImageSsFcc.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImageSsFccBigCell - Class in etomica.models.oneDHardRods
-
MC simulation
3D Lennard Jones
FCC crystal
No graphic display
uses single big cell approach
Calculate free energy of solid using normal mode insertion method
Treats coupling of modes as overlap variable;
Generate input files with HarmonicCrystalSoftSphereFCC
Uses overlap sampling.
- SimDifferentImageSsFccBigCell(Space, int[], int[], double, int, double, int, String, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell
-
- SimDifferentImageSsFccBigCell.SimParam - Class in etomica.models.oneDHardRods
-
- SimDifferentImageSsFccDoubleSize - Class in etomica.models.oneDHardRods
-
MC simulation
3D Lennard Jones
FCC crystal
No graphic display
uses single big cell approach
Calculate free energy of solid using normal mode insertion method
Treats coupling of modes as overlap variable;
Generate input files with HarmonicCrystalSoftSphereFCC
Uses overlap sampling.
- SimDifferentImageSsFccDoubleSize(Space, int[], int[], double, double, int, String, double) - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize
-
- SimDifferentImageSsFccDoubleSize.SimParam - Class in etomica.models.oneDHardRods
-
- SimDimerLJadatom - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom on a surface, modeled with LJ.
- SimDimerLJadatom() - Constructor for class etomica.dimer.SimDimerLJadatom
-
- SimDimerLJadatomCluster - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerLJadatomCluster(Space) - Constructor for class etomica.dimer.SimDimerLJadatomCluster
-
- SimDimerLJgb - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerLJgb() - Constructor for class etomica.dimer.SimDimerLJgb
-
- SimDimerMEAMadatom - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerMEAMadatom() - Constructor for class etomica.dimer.SimDimerMEAMadatom
-
- SimDimerMEAMadatomCluster - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerMEAMadatomCluster(Space) - Constructor for class etomica.dimer.SimDimerMEAMadatomCluster
-
- SimDimerMEAMGB - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerMEAMGB(int[], int[]) - Constructor for class etomica.dimer.SimDimerMEAMGB
-
- SimDimerMEAMGBCluster - Class in etomica.dimer
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimDimerMEAMGBCluster(Space) - Constructor for class etomica.dimer.SimDimerMEAMGBCluster
-
- SimDirectBetaN2RP - Class in etomica.models.nitrogen
-
Direct Sampling for Rotational Perturbation
- SimDirectBetaN2RP(Space, int, double, double, double[]) - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RP
-
- SimDirectBetaN2RP.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2RP constructor
- SimDirectBetaN2RPAngleToNoAngle - Class in etomica.models.nitrogen
-
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
- SimDirectBetaN2RPAngleToNoAngle(Space, int, double, double, double, long) - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
-
- SimDirectBetaN2RPInitPert - Class in etomica.models.nitrogen
-
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
- SimDirectBetaN2RPInitPert(Space, int, double, double, double, long) - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
-
- SimDirectDisorderedAlphaN2RPInitPert - Class in etomica.models.nitrogen
-
Direct Sampling for Rotational Perturbation
from NO rotational energy to constraint-angle rotational energy
- SimDirectDisorderedAlphaN2RPInitPert(Space, int, double, double, double, long) - Constructor for class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
-
- simEigenVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simEigenVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- SimEinStep1 - Class in etomica.normalmode
-
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
- SimEinStep1(Space, int, double, double, double, int, double, boolean) - Constructor for class etomica.normalmode.SimEinStep1
-
- SimEinStep1.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimEinStep1HCP - Class in etomica.normalmode
-
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
- SimEinStep1HCP(Space, int, double, double, double, int, double, double) - Constructor for class etomica.normalmode.SimEinStep1HCP
-
- SimEinStep1HCP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimEinStep2 - Class in etomica.normalmode
-
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
- SimEinStep2(Space, int, double, double, double, int, double, boolean) - Constructor for class etomica.normalmode.SimEinStep2
-
- SimEinStep2.MeterPotentialEnergyComposite - Class in etomica.normalmode
-
- SimEinStep2.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimEinStep2HCP - Class in etomica.normalmode
-
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
- SimEinStep2HCP(Space, int, double, double, double, int, double, double) - Constructor for class etomica.normalmode.SimEinStep2HCP
-
- SimEinStep2HCP.MeterPotentialEnergyComposite - Class in etomica.normalmode
-
- SimEinStep2HCP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimExtensiveTest - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Output: histogram files of probability that a mode is zero
Calculate free energy of solid
Testing whether or not using modes as degrees of freedom is extensive.
- SimExtensiveTest(Space, int, double, int, int) - Constructor for class etomica.models.oneDHardRods.SimExtensiveTest
-
- SimExtensiveTest.SimParam - Class in etomica.models.oneDHardRods
-
- SimFe - Class in etomica.freeenergy.npath
-
- SimFe(SimFe.Crystal, int, double, double, double, int, int, boolean, boolean, double) - Constructor for class etomica.freeenergy.npath.SimFe
-
- SimFe.LjMC3DParams - Class in etomica.freeenergy.npath
-
- SimFluidSoftSphere - Class in etomica.normalmode
-
MC simulation of soft-sphere fluid model
- SimFluidSoftSphere(Space, int, double, double, int) - Constructor for class etomica.normalmode.SimFluidSoftSphere
-
- simGraphic - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- SimHarmonic - Class in etomica.normalmode
-
Simulation to sample harmonic potential
- SimHarmonic(Space, int, double, String, double) - Constructor for class etomica.normalmode.SimHarmonic
-
- SimHarmonicHexane - Class in etomica.models.hexane
-
- SimHarmonicHexane(Space, double, int, int, int, String, double) - Constructor for class etomica.models.hexane.SimHarmonicHexane
-
- SimHarmonicUmbrella - Class in etomica.normalmode
-
Simulation to sample harmonic system and perturbing into
the umbrella sampling region
- SimHarmonicUmbrella(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimHarmonicUmbrella
-
- SimHarmonicUmbrella.SimBennetParam - Class in etomica.normalmode
-
- SimHSMDVacancy - Class in etomica.normalmode
-
Simple Lennard-Jones molecular dynamics simulation in 3D
- SimHSMDVacancy(int, double, double, int, int, double) - Constructor for class etomica.normalmode.SimHSMDVacancy
-
- SimHSMDVacancy.HSMDVParams - Class in etomica.normalmode
-
- SimIdealGas - Class in etomica.freeenergy.npath
-
Simple Lennard-Jones molecular dynamics simulation in 3D
- SimIdealGas(int, double, double, double, int) - Constructor for class etomica.freeenergy.npath.SimIdealGas
-
- SimIdealGas.LjMC3DParams - Class in etomica.freeenergy.npath
-
- simImagT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simImagT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- SimKMCLJadatom - Class in etomica.kmc
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom on a surface, modeled with LJ.
- SimKMCLJadatom() - Constructor for class etomica.kmc.SimKMCLJadatom
-
- SimKMCmaster - Class in etomica.kmc
-
- SimKMCmaster(Space) - Constructor for class etomica.kmc.SimKMCmaster
-
- SimKMCMEAMadatom - Class in etomica.kmc
-
Simulation using Henkelman's Dimer method to find a saddle point for
an adatom of Sn on a surface, modeled with MEAM.
- SimKMCMEAMadatom() - Constructor for class etomica.kmc.SimKMCMEAMadatom
-
- SimKMCworker - Class in etomica.kmc
-
- SimKMCworker(Space) - Constructor for class etomica.kmc.SimKMCworker
-
- SimLattice - Class in etomica.freeenergy.npath
-
Simple Lennard-Jones molecular dynamics simulation in 3D
- SimLattice(int, double, double, double, int) - Constructor for class etomica.freeenergy.npath.SimLattice
-
- SimLattice.LjMC3DParams - Class in etomica.freeenergy.npath
-
- SimLJ - Class in etomica.freeenergy.npath
-
Simple Lennard-Jones molecular dynamics simulation in 3D
- SimLJ(int, double, double, double, double, int) - Constructor for class etomica.freeenergy.npath.SimLJ
-
- SimLJ.LjMC3DParams - Class in etomica.freeenergy.npath
-
- SimLJHTTISuper - Class in etomica.normalmode
-
- SimLJHTTISuper(Space, int, double, double, double, boolean, int[]) - Constructor for class etomica.normalmode.SimLJHTTISuper
-
- SimLJHTTISuper.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimLJHTTISuperHCP - Class in etomica.normalmode
-
- SimLJHTTISuperHCP(Space, int, double, double, double, double, boolean, int[]) - Constructor for class etomica.normalmode.SimLJHTTISuperHCP
-
- SimLJHTTISuperHCP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimLJVacancy - Class in etomica.normalmode
-
Simple Lennard-Jones molecular dynamics simulation in 3D
- SimLJVacancy(int, double, double, double, int, double, boolean, boolean) - Constructor for class etomica.normalmode.SimLJVacancy
-
- SimLJVacancy.Applet - Class in etomica.normalmode
-
- SimLJVacancy.LJParams - Class in etomica.normalmode
-
- simModel - Variable in class etomica.meta.wrappers.Wrapper
-
- SimModesJ - Class in etomica.normalmode
-
Simulation class of hard spheres in 1D or 3D that calculates the dq/dx
Jacobian.
- SimModesJ(Space, int) - Constructor for class etomica.normalmode.SimModesJ
-
- SimOverlap - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlap(Space, int, double, double, String, double) - Constructor for class etomica.normalmode.SimOverlap
-
- SimOverlap.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapAlphaN2TP - Class in etomica.models.nitrogen
-
Temperature-perturbation simulation for alpha-phase Nitrogen
- SimOverlapAlphaN2TP(Space, int[], double, double, double[], double[], int, double, long, double, double, boolean) - Constructor for class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- SimOverlapAlphaN2TP.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapBetaN2RP - Class in etomica.models.nitrogen
-
- SimOverlapBetaN2RP(Space, int, double, double, double[], double, double, int) - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RP
-
- SimOverlapBetaN2RP.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2RP constructor
- SimOverlapBetaN2RPScaling - Class in etomica.models.nitrogen
-
rotational-perturbation simulation for beta-phase Nitrogen with angle scaling
however, one can set parameter "doScaling" to FALSE if scaling not desirable
- SimOverlapBetaN2RPScaling(Space, int, double, double, double[], double[], int, double, long, double, boolean) - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- SimOverlapBetaN2RPScaling.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
- SimOverlapBetaN2TP - Class in etomica.models.nitrogen
-
Temperature-perturbation simulation for beta-phase Nitrogen
- SimOverlapBetaN2TP(Space, int, double, double, double[], double[], int, double, long, boolean, boolean, double) - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- SimOverlapBetaN2TP.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
- SimOverlapDisorderedAlphaN2RPScaling - Class in etomica.models.nitrogen
-
rotational-perturbation simulation for beta-phase Nitrogen with angle scaling
however, one can set parameter "doScaling" to FALSE if scaling not desirable
- SimOverlapDisorderedAlphaN2RPScaling(Space, int, double, double, double[], double[], int, double, long, double, boolean) - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
- SimOverlapDisorderedAlphaN2TP - Class in etomica.models.nitrogen
-
Temperature-perturbation simulation for disordered alpha-phase Nitrogen
- SimOverlapDisorderedAlphaN2TP(Space, int, double, double, double[], double[], int, double, long, boolean, boolean, double) - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- SimOverlapDisorderedAlphaN2TP.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the SimOverlapBetaN2TP constructor
- SimOverlapLJ - Class in etomica.normalmode
-
Simulation to run sampling with the LJ potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapLJ(Space, int, double, double, double) - Constructor for class etomica.normalmode.SimOverlapLJ
-
- SimOverlapLJ.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapLJModule - Class in etomica.normalmode
-
Main method that constructs an overlap sampling module to calculate the free
energy difference between a harmonic system and a lennard jones solid.
- SimOverlapLJModule() - Constructor for class etomica.normalmode.SimOverlapLJModule
-
- SimOverlapLJModule.APIPotentialReference - Class in etomica.normalmode
-
- SimOverlapLJModule.APIPotentialTarget - Class in etomica.normalmode
-
- SimOverlapLJModule.MeterPotentialEnergyDifference - Class in etomica.normalmode
-
- SimOverlapLJModule.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapModule - Class in etomica.normalmode
-
Overlap sampling "module" to calculate free energy difference.
- SimOverlapModule(Box, Box, Integrator, Integrator, IAPIPotential, IAPIPotential, double) - Constructor for class etomica.normalmode.SimOverlapModule
-
- SimOverlapMultiHarmonic - Class in etomica.gaussianwork
-
MultiHarmonic Overlap Simulation
a.
- SimOverlapMultiHarmonic(int, double, double, double) - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- SimOverlapMultiHarmonic.SimOverlapParam - Class in etomica.gaussianwork
-
- SimOverlapMultiHarmonicOptRefPref - Class in etomica.gaussianwork
-
MultiHarmonic Overlap Simulation
a.
- SimOverlapMultiHarmonicOptRefPref(int, double, double, double, double) - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- SimOverlapMultiHarmonicOptRefPref.SimOverlapParam - Class in etomica.gaussianwork
-
- SimOverlapMultipleWaveVectors - Class in etomica.models.oneDHardRods
-
- SimOverlapMultipleWaveVectors(Space, int, double, double, String, double, int[], int[]) - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors
-
- SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam - Class in etomica.models.oneDHardRods
-
- SimOverlapMultipleWaveVectorsParam() - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- SimOverlapMultipleWaveVectorsParam() - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- SimOverlapMultipleWV3DLJ - Class in etomica.models.oneDHardRods
-
- SimOverlapMultipleWV3DLJ(Space, int, double, double, String, double, int[], int[]) - Constructor for class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ
-
- SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam - Class in etomica.models.oneDHardRods
-
- SimOverlapNitrogenModel - Class in etomica.models.nitrogen
-
Simulation to run sampling with the nitrogen model to find the free energy difference
between the harmonic reference system and the target system
The Bennett's Overlapping Sampling Simulation
- used to check for the computation time
- SimOverlapNitrogenModel(Space, int, double, String, double) - Constructor for class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- SimOverlapNitrogenModel.SimOverlapParam - Class in etomica.models.nitrogen
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapParam() - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.LJVacancyMin.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.MinimizeHCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlap.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapLJ.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- SimOverlapParam() - Constructor for class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
-
- SimOverlapSoftSphere - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphere(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphere
-
- SimOverlapSoftSphere.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereDP - Class in etomica.normalmode
-
Simulation to run density perturbation for soft spheres.
- SimOverlapSoftSphereDP(Space, int, boolean, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereDP
-
- SimOverlapSoftSphereDP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereEin - Class in etomica.normalmode
-
Simulation that samples a composite energy function (soft sphere and
Einstein crystal) and perturbs into overlap regions shared by systems with
more or less soft sphere contributions.
- SimOverlapSoftSphereEin(Space, int, double, boolean, double, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereEin
-
- SimOverlapSoftSphereEin.MeterPotentialEnergyComposite - Class in etomica.normalmode
-
- SimOverlapSoftSphereEin.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereEinHarm - Class in etomica.normalmode
-
Overlap sampling simulation whose target system has a composite energy
function (soft sphere and Einstein crystal) and whose reference system is
defined by (harmonically coupled) normal modes and Einstein crystal.
- SimOverlapSoftSphereEinHarm(Space, int, double, boolean, double, double, double, int, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereEinHarm
-
- SimOverlapSoftSphereEinHarm.MeterPotentialEnergyComposite - Class in etomica.normalmode
-
- SimOverlapSoftSphereEinHarm.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereHCP - Class in etomica.normalmode
-
Simulation to run sampling with the soft-sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphereHCP(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereHCP
-
- SimOverlapSoftSphereHCP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereReweighting - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphereReweighting(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereReweighting
-
- SimOverlapSoftSphereReweighting.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereSoftness - Class in etomica.normalmode
-
Conduct Bennett's Overlap Sampling to quantify the free-energy difference
between soft-sphere model with different softness
Soft-Sphere potential: U = epsilon*(sigma/r)^n
where n is the exponent, s = 1/n (where s is softness)
epsilon and sigma is set to 1
- SimOverlapSoftSphereSoftness(Space, int, double, double, double, int[], double, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereSoftness
-
- SimOverlapSoftSphereSoftness.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereSuperBox - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphereSuperBox(Space, int, double, double, String, double, int) - Constructor for class etomica.normalmode.SimOverlapSoftSphereSuperBox
-
- SimOverlapSoftSphereSuperBox.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereTP - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphereTP(Space, int, boolean, boolean, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereTP
-
- SimOverlapSoftSphereTP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereTPHCP - Class in etomica.normalmode
-
The original Bennett's Overlapping Sampling Simulation
- used to check for the computation time
- SimOverlapSoftSphereTPHCP(Space, int, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPHCP
-
- SimOverlapSoftSphereTPHCP.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSoftSphereTPSlantedBox - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSoftSphereTPSlantedBox(Space, int, double, double, double[], double[], int, int, double, long, double) - Constructor for class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox
-
- SimOverlapSoftSphereTPSlantedBox.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSsNxy - Class in etomica.models.oneDHardRods
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSsNxy(Space, int, double, double, String, double, int, int[], double) - Constructor for class etomica.models.oneDHardRods.SimOverlapSsNxy
-
- SimOverlapSSnxy - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimOverlapSSnxy(Space, int, double, double, String, double, int, int[]) - Constructor for class etomica.normalmode.SimOverlapSSnxy
-
- SimOverlapSsNxy.SimOverlapParam - Class in etomica.models.oneDHardRods
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapSSnxy.SimOverlapParam - Class in etomica.normalmode
-
Inner class for parameters understood by the HSMD3D constructor
- SimOverlapTPSSParams() - Constructor for class etomica.normalmode.HTTPSoftSphereApplet.SimOverlapTPSSParams
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.SimWidomMode.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- SimParam() - Constructor for class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
-
- SimParams() - Constructor for class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- SimParams() - Constructor for class etomica.models.clathrates.MinimizationTIP4P.SimParams
-
- SimParams() - Constructor for class etomica.tests.TestHSMD3D.SimParams
-
- SimParams() - Constructor for class etomica.tests.TestLJGCMC3D.SimParams
-
- SimParams() - Constructor for class etomica.tests.TestLJMC3D.SimParams
-
- SimParams() - Constructor for class etomica.tests.TestSWChain.SimParams
-
- simple(String, double) - Static method in class etomica.atom.AtomType
-
Convenience factory method for creating an AtomType with a one-off ElementSimple.
- Simple() - Constructor for class etomica.graphics.ColorScheme.Simple
-
- Simple(Color) - Constructor for class etomica.graphics.ColorScheme.Simple
-
- SimpleElementForSimilarSpecies - Class in etomica.virial.GUI.components
-
- simpleReplace(String, String, String) - Static method in class org.jmol.util.TextFormat
-
Does a clean replace of strFrom in str with strTo
If strTo contains strFrom, then only a single pass is done.
- SimpleUnit - Class in etomica.units
-
Superclass for all base unit classes.
- SimpleUnit(Dimension, double, String, String, boolean) - Constructor for class etomica.units.SimpleUnit
-
- simplifiedP3NonAdd - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- simplifiedP3NonAdd - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- simplify() - Method in class etomica.math.Rational
-
Simplify the rational.
- simplify() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Simplify the representation.
- simRealT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simRealT - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- SimTarget - Class in etomica.normalmode
-
Simulation to run sampling with the hard sphere potential, but measuring
the harmonic potential based on normal mode data from a previous simulation.
- SimTarget(Space, int, double) - Constructor for class etomica.normalmode.SimTarget
-
- SimTargetUmbrella - Class in etomica.normalmode
-
Simulation to sample target system and perturbing into
the umbrella sampling region
- SimTargetUmbrella(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimTargetUmbrella
-
- SimTargetUmbrella.SimBennetParam - Class in etomica.normalmode
-
- simType - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- simType - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- simulation - Variable in class etomica.action.SimulationActionAdapter
-
- simulation - Variable in class etomica.graphics.SimulationGraphic
-
- simulation - Variable in class etomica.modules.chainequilibrium.ColorSchemeStepWise
-
- simulation - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- simulation - Variable in class etomica.nbr.PotentialMasterNbr
-
- Simulation - Class in etomica.simulation
-
The main class that organizes the elements of a molecular simulation.
- Simulation(Space) - Constructor for class etomica.simulation.Simulation
-
Creates a new simulation using the given space
- SimulationAction - Interface in etomica.action
-
Interface for classes that apply some elementary action (transformation) to a
simulation.
- SimulationActionAdapter - Class in etomica.action
-
Convenience class used to define a SimulationAction.
- SimulationActionAdapter() - Constructor for class etomica.action.SimulationActionAdapter
-
- SimulationAlphaNitrogenModel - Class in etomica.models.nitrogen
-
Simulation class for nitrogen molecules
alpha-N2 crystal Structure
- SimulationAlphaNitrogenModel(Space, int[], double, double) - Constructor for class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- SimulationAtomTypeEvent - Class in etomica.simulation
-
- SimulationAtomTypeEvent(Simulation, AtomType) - Constructor for class etomica.simulation.SimulationAtomTypeEvent
-
- simulationAtomTypeIndexChanged(SimulationAtomTypeIndexEvent) - Method in class etomica.atom.AtomTypeAgentManager
-
- simulationAtomTypeIndexChanged(SimulationAtomTypeIndexEvent) - Method in interface etomica.simulation.SimulationListener
-
- SimulationAtomTypeIndexEvent - Class in etomica.simulation
-
- SimulationAtomTypeIndexEvent(Simulation, AtomType, int) - Constructor for class etomica.simulation.SimulationAtomTypeIndexEvent
-
- simulationAtomTypeMaxIndexChanged(SimulationIndexEvent) - Method in interface etomica.simulation.SimulationListener
-
- SimulationBetaNitrogenModel - Class in etomica.models.nitrogen
-
Simulation class for nitrogen molecules
beta-N2 crystal Structure
- SimulationBetaNitrogenModel(Space, int, double, double) - Constructor for class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- SimulationBetaNitrogenModelTest - Class in etomica.models.nitrogen
-
Simulation class for nitrogen molecules
beta-N2 crystal Structure
- SimulationBetaNitrogenModelTest(Space, int[], double, double, double) - Constructor for class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- simulationBoxAdded(SimulationBoxEvent) - Method in class etomica.box.BoxAgentManager
-
- simulationBoxAdded(SimulationBoxEvent) - Method in interface etomica.simulation.SimulationListener
-
- SimulationBoxEvent - Class in etomica.simulation
-
- SimulationBoxEvent(Simulation, Box) - Constructor for class etomica.simulation.SimulationBoxEvent
-
- simulationBoxRemoved(SimulationBoxEvent) - Method in class etomica.box.BoxAgentManager
-
- simulationBoxRemoved(SimulationBoxEvent) - Method in interface etomica.simulation.SimulationListener
-
- SimulationConstructor - Class in etomica.server.representations
-
- SimulationConstructor() - Constructor for class etomica.server.representations.SimulationConstructor
-
- SimulationContainer - Interface in etomica.simulation
-
TODO To change the template for this generated type comment go to
Window - Preferences - Java - Code Style - Code Templates
- SimulationDataAction - Class in etomica.action
-
Action that performs a call to the reset() method of a set
of accumulators, as specified via a list of AccumulatorManager
instances.
- SimulationDataAction(DataStreamAction) - Constructor for class etomica.action.SimulationDataAction
-
- SimulationEvent - Class in etomica.simulation
-
- SimulationEvent(Simulation) - Constructor for class etomica.simulation.SimulationEvent
-
- SimulationEventManager - Class in etomica.simulation
-
- SimulationEventManager(Simulation) - Constructor for class etomica.simulation.SimulationEventManager
-
- SimulationGammaNitrogenModel - Class in etomica.models.nitrogen
-
Simulation class for nitrogen molecules
gamma-N2 crystal Structure
- SimulationGammaNitrogenModel(Space, int, double, double) - Constructor for class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- SimulationGraphic - Class in etomica.graphics
-
General class for graphical presentation of the elements of a molecular simulation.
- SimulationGraphic(Simulation) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationGraphic(Simulation, int) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationGraphic(Simulation, String) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationGraphic(Simulation, int, String) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationGraphic(Simulation, String, int) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationGraphic(Simulation, int, String, int) - Constructor for class etomica.graphics.SimulationGraphic
-
- SimulationIndexEvent - Class in etomica.simulation
-
- SimulationIndexEvent(Simulation, int) - Constructor for class etomica.simulation.SimulationIndexEvent
-
- SimulationListener - Interface in etomica.simulation
-
- SimulationModel - Class in etomica.meta
-
- SimulationModel(Simulation) - Constructor for class etomica.meta.SimulationModel
-
- SimulationOrthorhombicParacetamol - Class in etomica.paracetamol
-
Simulation of 3D Paracetamol molecules in Form II (Orthorhombic)
- SimulationOrthorhombicParacetamol(Space, int, double) - Constructor for class etomica.paracetamol.SimulationOrthorhombicParacetamol
-
- SimulationPanel - Class in etomica.graphics
-
Main panel used to display the graphical elements of a simulation.
- SimulationPanel() - Constructor for class etomica.graphics.SimulationPanel
-
- SimulationPanel(String) - Constructor for class etomica.graphics.SimulationPanel
-
- SimulationResource - Class in etomica.server.resources
-
- SimulationResource(SimulationStore, DataStreamStore) - Constructor for class etomica.server.resources.SimulationResource
-
- SimulationRestart - Class in etomica.action
-
Action that invokes reset method of all registered simulation elements,
effectively initializing the entire simulation.
- SimulationRestart(Simulation) - Constructor for class etomica.action.SimulationRestart
-
- SimulationRheology - Class in etomica.modules.rheology
-
Simulation for rheology module.
- SimulationRheology(Space) - Constructor for class etomica.modules.rheology.SimulationRheology
-
- SimulationRunner - Class in etomica.virial.GUI.components
-
- SimulationRunner(ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.components.SimulationRunner
-
- SimulationsIndexResource - Class in etomica.server.resources
-
- SimulationsIndexResource(ComponentIndex<Simulation>, SimulationStore) - Constructor for class etomica.server.resources.SimulationsIndexResource
-
- simulationSpeciesAdded(SimulationSpeciesEvent) - Method in class etomica.atom.AtomTypeAgentManager
-
- simulationSpeciesAdded(SimulationSpeciesEvent) - Method in class etomica.molecule.MoleculeAgentManager
-
- simulationSpeciesAdded(SimulationSpeciesEvent) - Method in interface etomica.simulation.SimulationListener
-
- SimulationSpeciesEvent - Class in etomica.simulation
-
- SimulationSpeciesEvent(Simulation, ISpecies) - Constructor for class etomica.simulation.SimulationSpeciesEvent
-
- simulationSpeciesIndexChanged(SimulationSpeciesIndexEvent) - Method in interface etomica.simulation.SimulationListener
-
- SimulationSpeciesIndexEvent - Class in etomica.simulation
-
- SimulationSpeciesIndexEvent(Simulation, ISpecies, int) - Constructor for class etomica.simulation.SimulationSpeciesIndexEvent
-
- simulationSpeciesMaxIndexChanged(SimulationIndexEvent) - Method in interface etomica.simulation.SimulationListener
-
- simulationSpeciesRemoved(SimulationSpeciesEvent) - Method in class etomica.atom.AtomTypeAgentManager
-
- simulationSpeciesRemoved(SimulationSpeciesEvent) - Method in class etomica.molecule.MoleculeAgentManager
-
- simulationSpeciesRemoved(SimulationSpeciesEvent) - Method in interface etomica.simulation.SimulationListener
-
- SimulationStore - Class in etomica.server.dao
-
- SimulationStore() - Constructor for class etomica.server.dao.SimulationStore
-
- SimulationVirial - Class in etomica.virial.simulations
-
Generic simulation using Mayer sampling to evaluate cluster integrals
- SimulationVirial(Space, ISpecies[], int[], double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirial
-
- SimulationVirial(Space, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirial
-
Constructor for simulation to determine the ratio between reference and target Clusters
- SimulationVirial(Space, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirial
-
- SimulationVirial(Space, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirial
-
- SimulationVirial(Space, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirial
-
- SimulationVirial(Space, ISpecies, double, ClusterWeight, ClusterAbstract, ClusterAbstract[], boolean, int[]) - Constructor for class etomica.virial.simulations.SimulationVirial
-
- SimulationVirialDiagram - Class in etomica.virial.simulations
-
Virial simulation using diagram sampling.
- SimulationVirialDiagram(Space, SpeciesFactory, double, ClusterWeight, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirialDiagram
-
- SimulationVirialMultiOverlap - Class in etomica.virial.simulations
-
- SimulationVirialMultiOverlap(Space, SpeciesFactory[], double, ClusterAbstract, ClusterAbstract, int[]) - Constructor for class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- SimulationVirialMultiOverlap(Space, SpeciesFactory[], double, ClusterAbstract, ClusterAbstract, boolean, int[]) - Constructor for class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- SimulationVirialMultiOverlap(Space, SpeciesFactory[], double, ClusterAbstract[], ClusterWeight[], boolean, int[]) - Constructor for class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- SimulationVirialOverlap - Class in etomica.virial.simulations
-
- SimulationVirialOverlap(Space, SpeciesFactory, double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
-
- SimulationVirialOverlap(Space, SpeciesFactory, double, ClusterAbstract, ClusterAbstract, boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
-
- SimulationVirialOverlap(Space, SpeciesFactory, double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
-
- SimulationVirialOverlap(Space, SpeciesFactory[], int[], double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap
-
- SimulationVirialOverlap2 - Class in etomica.virial.simulations
-
Simulation implementing the overlap-sampling approach to evaluating a cluster
diagram.
- SimulationVirialOverlap2(Space, ISpecies, int, double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
This constructor will create your simulation class, but you may call
set methods before using it.
- SimulationVirialOverlap2(Space, ISpecies[], int[], double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
This constructor will create your simulation class, but you may call
set methods before using it.
- SimulationVirialOverlap2(Space, ISpecies, double, ClusterAbstract, ClusterAbstract) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
- SimulationVirialOverlap2(Space, ISpecies, double, ClusterAbstract, ClusterAbstract, boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
- SimulationVirialOverlap2(Space, ISpecies, double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
- SimulationVirialOverlap2(Space, ISpecies[], int[], double, ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
- SimulationVirialOverlap2(Space, ISpecies[], int[], double, ClusterAbstract[], ClusterAbstract[], ClusterWeight[], boolean) - Constructor for class etomica.virial.simulations.SimulationVirialOverlap2
-
- SimulationVirialOverlap2.BoxClusterFactory - Class in etomica.virial.simulations
-
- SimulationVirialUmbrella - Class in etomica.virial.simulations
-
Simulation implementing the umbrella-sampling approach to evaluating a cluster
diagram.
- SimulationVirialUmbrella(Space, double, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirialUmbrella
-
- SimulationVirialUmbrella(Space, SpeciesFactory, double, ClusterAbstract, ClusterAbstract[]) - Constructor for class etomica.virial.simulations.SimulationVirialUmbrella
-
- SimulationWorker(int, int, int, MayerFunction, MayerFunction, int, double, double, double, long, Space, String, double, Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, double, long[], boolean, int[], boolean) - Constructor for class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- SimulationWorker(int, int, MayerFunction, MayerFunction, MayerFunction, double, double, double, double, long, Space, String, double, Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, double, long[], boolean, int[], boolean, double) - Constructor for class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- SimulationWrapper - Class in etomica.meta.wrappers
-
Specialized wrapper for Simulations.
- SimulationWrapper(Simulation, SimulationModel, boolean) - Constructor for class etomica.meta.wrappers.SimulationWrapper
-
- SimUmbrella - Class in etomica.normalmode
-
Simulation to sample Umbrella Sampling
- SimUmbrella(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimUmbrella
-
- SimUmbrella.SimBennetParam - Class in etomica.normalmode
-
- SimUmbrellaSoftSphere - Class in etomica.normalmode
-
Simulation to sample Umbrella Overlap Sampling
The original Umbrella Sampling Simulation
- used to check for the computation time
- SimUmbrellaSoftSphere(Space, int, double, double, String, int) - Constructor for class etomica.normalmode.SimUmbrellaSoftSphere
-
- SimUmbrellaSoftSphere.SimBennetParam - Class in etomica.normalmode
-
- simWaveVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simWaveVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- SimWidomMode - Class in etomica.models.oneDHardRods
-
MD simulation of hard spheres in 1D or 3D with tabulation of the
collective-coordinate S-matrix.
- SimWidomMode(Space, int, double, int) - Constructor for class etomica.models.oneDHardRods.SimWidomMode
-
- SimWidomMode.SimParam - Class in etomica.models.oneDHardRods
-
- simWVCoeff - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- simWVCoeff - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- sin() - Method in class etomica.math.Complex
-
Sine of this Complex number (doesn't change this Complex number).
- sin(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Trigonometric sine.
- sinDtheta - Variable in class etomica.dimer.IntegratorDimerMin
-
- SineTransform - Class in etomica.math.numerical
-
3D Fourier transforms of a function, f, simplify to 1D sine transforms of the auxiliary function F(r) = r*f(r)
when f is spherically symmetric.
- SineTransform() - Constructor for class etomica.math.numerical.SineTransform
-
- sinGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal
-
- sinGamma - Static variable in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- singleAction - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- singleAction - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- singleAction - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- singleAction - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- SingleAssociationSiteFluid - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid
-
- SingleAssociationSiteFluid.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid2 - Class in etomica.virial.simulations
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
- SingleAssociationSiteFluid2() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid2
-
- SingleAssociationSiteFluid2.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid2Pt - Class in etomica.virial.simulations
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
2points and 3 points diagram calculation
- SingleAssociationSiteFluid2Pt() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid2Pt
-
- SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid3Pt - Class in etomica.virial.simulations
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
2points and 3 points diagram calculation
- SingleAssociationSiteFluid3Pt() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid3Pt
-
- SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid4Points - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid4Points() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid4Points
-
- SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluid4Pt - Class in etomica.virial.simulations
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's double attraction-site model
4points diagram calculation
- SingleAssociationSiteFluid4Pt() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid4Pt
-
- SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleAssociationSiteFluidGraph - Class in etomica.virial.simulations
-
repulsive potential: Lennard-Jones potential
attractive potential: short-handed square well potential
Wertheim's single attraction-site model
- SingleAssociationSiteFluidGraph() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluidGraph
-
- SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- SingleDipole - Class in etomica.rotation
-
- SingleDipole() - Constructor for class etomica.rotation.SingleDipole
-
- SingleDipole.Applet - Class in etomica.rotation
-
- SingleDumbellRattle - Class in etomica.rotation
-
- SingleDumbellRattle() - Constructor for class etomica.rotation.SingleDumbellRattle
-
- SingleDumbellRattle.Applet - Class in etomica.rotation
-
- SingleDumbellShake - Class in etomica.rotation
-
- SingleDumbellShake() - Constructor for class etomica.rotation.SingleDumbellShake
-
- SingleDumbellShake.Applet - Class in etomica.rotation
-
- singlet - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- singlet - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- singletId(int, int) - Static method in class etomica.virial.cluster.VirialDiagrams
-
- SingleValueOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.SingleValueOptionHandler
-
- SingleWater - Class in etomica.rotation
-
- SingleWater() - Constructor for class etomica.rotation.SingleWater
-
- SingleWater.Applet - Class in etomica.rotation
-
- SingleWaterMatrix - Class in etomica.rotation
-
- SingleWaterMatrix() - Constructor for class etomica.rotation.SingleWaterMatrix
-
- SingleWaterMatrix.Applet - Class in etomica.rotation
-
- SingleWaterRattle - Class in etomica.rotation
-
- SingleWaterRattle() - Constructor for class etomica.rotation.SingleWaterRattle
-
- SingleWaterRattle.Applet - Class in etomica.rotation
-
- SingleWaterShake - Class in etomica.rotation
-
- SingleWaterShake() - Constructor for class etomica.rotation.SingleWaterShake
-
- SingleWaterShake.Applet - Class in etomica.rotation
-
- sinh() - Method in class etomica.math.Complex
-
Hyperbolic sine of this Complex number
(doesn't change this Complex number).
- sinh(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The hyperbolic sine.
- sink - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- sink - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- sink0 - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- sink0 - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- sinkDy - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- sinkDy - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- sinkDy2 - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- sinkDy2 - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- sinkDy3 - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- sinkEigen - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- sinkEy - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- sinkEy - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- sinkrj - Variable in class etomica.potential.EwaldSummation
-
- sinkSmoothed - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- sinkSmoothed - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- sinkTrue - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- sinkTrueEy - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- sinkWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- sinTheta - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- sinTheta - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- sinusoidalB - Variable in class etomica.modules.sam.Sam
-
- site(int[]) - Method in class etomica.config.ConfigurationLattice.MyLattice
-
Returns the same instance of Vector with each call.
- site(int[]) - Method in interface etomica.lattice.AbstractLattice
-
Returns the site specified by the given index.
- site(int[]) - Method in class etomica.lattice.BravaisLattice
-
Calculates and returns a vector that is the spatial position given
by adding together the primitive vectors, each multiplied by the corresponding
integer index given by the array argument.
- site(int[]) - Method in class etomica.lattice.BravaisLatticeCrystal
-
Returns a Vector instance giving the location of the referenced site.
- site(Vector) - Method in class etomica.lattice.CellLattice
-
Returns the cell in which the given point lies.
- site(int[]) - Method in class etomica.lattice.RectangularLattice
-
Returns the instance of the object associated with the given index.
- site(int[]) - Method in class etomica.paracetamol.ConfigurationMonoclinicLattice.MyLattice
-
Returns the same instance of Vector with each call.
- site(int[]) - Method in class etomica.paracetamol.ConfigurationOrthorhombicLattice.MyLattice
-
Returns the same instance of Vector with each call.
- site - Static variable in class org.jmol.script.Token
-
- siteat - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- sitebt - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- siteDisplacement - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- siteDisplacement - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- siteDoubles - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- siteFactor - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- siteFactory - Variable in class etomica.lattice.RectangularLattice
-
- SiteFactory - Interface in etomica.lattice
-
Interface for a class that generates the sites populating a lattice.
- siteID - Static variable in class etomica.models.co2.P2CO2Hellmann
-
- siteID - Static variable in class etomica.potential.P2NitrogenHellmann
-
- siteID - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- SiteIterator - Interface in etomica.lattice
-
Interface for objects that iterate over some or all of the
sites of a lattice.
- siteManager - Variable in class etomica.normalmode.CoordinateDefinition
-
- sitePos - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- sitePos - Variable in class etomica.models.water.P2WaterSzalewicz
-
- sitePos3 - Variable in class etomica.models.water.P2WaterSzalewicz
-
- sitePosA - Static variable in class etomica.potential.P2NitrogenHellmann
-
- sitePosA - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- sitePosB - Static variable in class etomica.potential.P2NitrogenHellmann
-
- sitePosB - Static variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- sites() - Method in interface etomica.lattice.FiniteLattice
-
Returns an array containing all the sites in the lattice.
- sites - Variable in class etomica.lattice.RectangularLattice
-
- sites() - Method in class etomica.lattice.RectangularLattice
-
- sites - Static variable in class etomica.models.water.P2WaterSzalewicz
-
- sitesCO2L - Static variable in class etomica.models.co2.P2CO2H2OWheatley
-
- sitesHH - Static variable in class etomica.models.co2.P2CO2H2OWheatley
-
- sitesOH - Static variable in class etomica.models.co2.P2CO2H2OWheatley
-
- SiteSource(Space) - Constructor for class etomica.normalmode.CoordinateDefinition.SiteSource
-
- sixId(int, int, int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams
-
Returns the six-molecule ID for the given indices (id0, id1, id2, id3, id4, id5)
and given number of molecules (n).
- sixId(int, int, int, int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagramsPT
-
Returns the six-molecule ID for the given indices (id0, id1, id2, id3, id4, id5)
and given number of molecules (n).
- sixStart - Static variable in class etomica.virial.cluster.VirialDiagrams
-
- sixStart - Static variable in class etomica.virial.cluster.VirialDiagramsPT
-
- size() - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
- size() - Method in class etomica.atom.iterator.ANIntergroupExchange
-
- size() - Method in class etomica.atom.iterator.ANIntragroupExchange
-
- size() - Method in class etomica.atom.iterator.ApiIndexList
-
- size() - Method in class etomica.atom.iterator.ApiInnerVariable
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.atom.iterator.ApiInterArrayList
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.atom.iterator.ApiIntergroup
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.atom.iterator.ApiIntergroupCoupled
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.atom.iterator.ApiIntergroupExchange
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.atom.iterator.ApiIntraArrayList
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.atom.iterator.ApiIntragroup
-
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
- size() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
Returns the number of iterates given by this iterator, if iterated after
a call to reset().
- size() - Method in class etomica.atom.iterator.AtomIteratorArrayList
-
Returns the number of iterates that would be given by this iterator
if reset with the current list.
- size() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
Returns the number of iterates that iterator would give
if reset and iterated in its current condition.
- size() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Returns the number of iterates that would be given by this iterator
if reset with the current list.
- size() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType
-
- size() - Method in class etomica.atom.iterator.AtomIteratorBasisFilteredType2
-
- size() - Method in class etomica.atom.iterator.AtomIteratorLeafFilteredType
-
- size() - Method in class etomica.atom.iterator.AtomIteratorNull
-
- size() - Method in class etomica.atom.iterator.AtomIteratorSinglet
-
returns 1 if atom is not null, 0 if atom is null.
- size() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
- size() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
- size() - Method in interface etomica.atom.iterator.AtomsetIterator
-
The number of iterates returned by this iterator in its current state.
- size() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
Returns the number of iterates given by this iterator, if iterated after
a call to reset().
- size() - Method in class etomica.atom.iterator.TripletInnerSequential
-
- size() - Method in class etomica.graph.model.GraphList
-
- size() - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- size() - Method in class etomica.graph.operations.RelabelParameters
-
- size() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- size() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- size() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- size - Variable in class etomica.lattice.crystal.Primitive
-
- size() - Method in class etomica.lattice.RectangularLattice.Iterator
-
- size - Variable in class etomica.lattice.RectangularLattice
-
- size() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
The number of iterates returned by this iterator in its current state.
- size() - Method in interface etomica.lattice.SiteIterator
-
Returns the number of iterates that this iterator would give
if reset.
- size - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- size - Variable in class etomica.modules.droplet.DropletGraphic.ModifierBoxSize
-
- size - Variable in class etomica.modules.interfacial.InterfacialSWGraphic.ModifierBoxSize
-
- size() - Method in class etomica.modules.pistoncylinder.ApiFilteredCylinder
-
- size() - Method in class etomica.molecule.iterator.MoleculeIteratorAll
-
Returns the number of iterates given by this iterator, if iterated after
a call to reset().
- size() - Method in class etomica.molecule.iterator.MoleculeIteratorArrayList
-
Returns the number of iterates that would be given by this iterator
if reset with the current list.
- size() - Method in class etomica.molecule.iterator.MoleculeIteratorArrayListSimple
-
Returns the number of iterates that would be given by this iterator
if reset with the current list.
- size() - Method in class etomica.molecule.iterator.MoleculeIteratorSinglet
-
returns 1 if atom is not null, 0 if atom is null.
- size() - Method in class etomica.molecule.iterator.MpiInnerFixed
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.molecule.iterator.MpiInnerVariable
-
Returns the number of pairs given by this iterator.
- size() - Method in class etomica.molecule.iterator.MpiInterArrayList
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.molecule.iterator.MpiInterspecies1A
-
- size() - Method in class etomica.molecule.iterator.MpiInterspeciesAA
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.molecule.iterator.MpiIntraArrayList
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.molecule.iterator.MpiIntraspecies1A
-
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
- size() - Method in class etomica.molecule.iterator.MpiIntraspeciesAA
-
Returns the number of iterates, which is list.size*(list.size-1)/2
- size() - Method in class etomica.molecule.iterator.MpiMolecule
-
Returns the number of iterates that would be given
when iterating after reset.
- size() - Method in class etomica.nbr.cell.Api1ACell
-
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
- size() - Method in class etomica.nbr.cell.ApiAACell
-
Returns the number of atom pairs the iterator will return if reset and
iterated in its present state.
- size() - Method in class etomica.nbr.cell.AtomIteratorCell
-
Returns the number of atoms the iterator will return if reset and
iterated in its present state.
- size() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
Returns the number of atoms the iterator will return if reset and
iterated in its present state.
- size() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
- size() - Method in class etomica.nbr.cell.molecule.MpiAACell
-
Returns the number of atom pairs the iterator will return if reset and
iterated in its present state.
- size() - Method in class etomica.nbr.site.Api1ASite
-
Returns the number of atom pairs the iterator will return if
reset and iterated in its present state.
- size() - Method in class etomica.potential.P2HardBondedList.BondArrayList
-
- size() - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- size() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- size() - Method in class etomica.util.collections.IndexMap
-
- size() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Count of coefficients.
- size() - Method in class org.jmol.util.BitSet
-
Returns the number of bits of space actually in use by this BitSet
to represent bit values.
- sizeCellX - Variable in class etomica.modules.sam.Sam
-
- sizeCellZ - Variable in class etomica.modules.sam.Sam
-
- sizeOf(Token) - Static method in class org.jmol.script.ScriptVariable
-
- sizeOfArray() - Method in class etomica.atom.AtomArrayList
-
- sizeOfArray() - Method in class etomica.molecule.MoleculeArrayList
-
- sizePanel - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- skew - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- skew - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- SKEW - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- SKEW - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- slab - Static variable in class org.jmol.script.Token
-
- slab - Variable in class org.jmol.util.GData
-
- slabBrillouin(Point3f[]) - Method in class org.jmol.util.MeshSurface
-
- slabbyatom - Static variable in class org.jmol.script.Token
-
- slabbymolecule - Static variable in class org.jmol.script.Token
-
- slabColix - Variable in class org.jmol.util.MeshSurface
-
- slabenabled - Static variable in class org.jmol.script.Token
-
- slabMeshType - Variable in class org.jmol.util.MeshSurface
-
- slabOptions - Variable in class org.jmol.util.MeshSurface
-
- slabPolygons(Object[], boolean) - Method in class org.jmol.util.MeshSurface
-
- slabPolygonsList(List<Object[]>, boolean) - Method in class org.jmol.util.MeshSurface
-
- slabrange - Static variable in class org.jmol.script.Token
-
- slabValue - Variable in class g3dsys.control.TransformManager
-
- slanty - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- slanty - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- slanty - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- slider - Variable in class etomica.graphics.DeviceSlider
-
Subclass of Swing slider displayed to screen
located in utility package
- sliderA - Variable in class etomica.modules.rheology.RheologyGraphic
-
- sliders(int, int, String, P2SquareWellBonded) - Method in class etomica.modules.chainequilibrium.ChainEquilibriumGraphic
-
- sliders(int, int, String, P2SquareWellBonded) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
-
- sliders(int, int, String, P2SquareWellRadical[]) - Method in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationGraphic
-
- smallmoleculemaxatoms - Static variable in class org.jmol.script.Token
-
- smartaromatic - Static variable in class org.jmol.script.Token
-
- smerList - Variable in class etomica.association.ColorSchemeSmer.ColorAgent
-
- smerList - Variable in class etomica.association.ColorSchemeSmer
-
- smerList - Variable in class etomica.association.ColorSchemeSmerByLength
-
- smerList - Variable in class etomica.association.MCMoveAtomMonomer
-
- smerList - Variable in class etomica.association.MCMoveAtomSmer
-
- smerList - Variable in class etomica.association.MCMoveBiasUB
-
- smerList - Variable in class etomica.association.MCMoveBiasUBMolecule
-
- smerList - Variable in class etomica.association.MCMoveMoleculeMonomer
-
- smerList - Variable in class etomica.association.MCMoveMoleculeRotateAssociated
-
- smerList - Variable in class etomica.association.MCMoveMoleculeSmer
-
- smerList - Variable in class etomica.association.MCMoveRotateAssociated
-
- smerList - Variable in class etomica.association.MCMoveSmer
-
- smerList - Variable in class etomica.association.MCMoveSmerRotate
-
- smerList - Variable in class etomica.association.MCMoveVolumeAssociated
-
- smerList - Variable in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- smiles2dimageformat - Static variable in class org.jmol.script.Token
-
- smilesurlformat - Static variable in class org.jmol.script.Token
-
- sn - Variable in class etomica.dimer.EnergyMap
-
- sn - Variable in class etomica.meam.MEAM_MC
-
- sn - Variable in class etomica.meam.MEAMMd3D
-
- Sn - Static variable in class etomica.meam.ParameterSetMEAM
-
- sn - Variable in class etomica.threaded.domain.MEAMMd3DThreaded
-
- snA - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- snA - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- snA - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- snAdatom - Variable in class etomica.dimer.EnergyMap
-
- snapshotAnaglyphChannelBytes() - Method in class org.jmol.g3d.Graphics3D
-
- snapshotAnaglyphChannelBytes() - Method in class org.jmol.util.GData
-
- snapshotTime - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Document time to seek to.
- snB - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- snFix - Variable in class etomica.dimer.EnergyMap
-
- snFixedA - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- snFixedA - Variable in class etomica.meam.MEAM_3DMDwithSnAgGB
-
- snFixedA - Variable in class etomica.meam.MEAM_3DMDwithSnCuGB
-
- snFixedB - Variable in class etomica.meam.MEAM_3DMDwithGB
-
- so2 - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- Sodium - Class in etomica.chem.elements
-
Class for the Sodium element.
- Sodium(String) - Constructor for class etomica.chem.elements.Sodium
-
- Sodium(String, double) - Constructor for class etomica.chem.elements.Sodium
-
- SoftBDcount - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- SoftSphere3d - Class in etomica.simulation.prototypes
-
Simple soft-sphere Monte Carlo simulation in 3D.
- SoftSphere3d() - Constructor for class etomica.simulation.prototypes.SoftSphere3d
-
- SoftSphere3d(double, int, double) - Constructor for class etomica.simulation.prototypes.SoftSphere3d
-
- SoftSphereSolidEOS - Class in etomica.normalmode
-
Soft-Sphere Solid Equation of State
for n = 12, 9 and 6
Reference: Tan, Schultz and Kofke, J Chem.
- SoftSphereSolidEOS() - Constructor for class etomica.normalmode.SoftSphereSolidEOS
-
- SoftSphereSolidEOSCalculator - Class in etomica.normalmode
-
- SoftSphereSolidEOSCalculator() - Constructor for class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- soluteChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- soluteChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- soluteChargeSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- soluteMoleFraction - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- soluteMoleFraction - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- soluteMoleFractionSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- soluteMoleFractionSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- solutionChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- solutionChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- solve(BigInteger[][], BigInteger[]) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Solve a linear system of equations.
- solveCoefficients() - Method in class etomica.math.numerical.PadeApproximation
-
- solvent - Static variable in class org.jmol.script.Token
-
- solventChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- solventChamberDensity - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- solventChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- solventChamberDensitySlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- solventprobe - Static variable in class org.jmol.script.Token
-
- solventproberadius - Static variable in class org.jmol.script.Token
-
- solventThermoFrac - Variable in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
- sort() - Method in class etomica.graph.model.GraphList
-
- sort(int[], int) - Method in class etomica.graph.property.FactorFFT
-
- sort() - Method in class etomica.virial.cluster.ClusterDiagram
-
Sorts list of connections for each node in the diagram such that
mConnections[i][j] < mConnections[i][k] for k > j.
- sort - Static variable in class org.jmol.g3d.Graphics3D
-
- Sort(int) - Constructor for class org.jmol.script.ScriptVariable.Sort
-
- sortConnections(ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations
-
- sortDiagrams(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Sorts diagrams in order from most bonds to fewest bonds
- sorted - Variable in class etomica.graph.model.GraphList
-
- sortedItem(List<String>, int) - Static method in class org.jmol.util.ArrayUtil
-
- sortKey - Variable in class etomica.util.TreeLinker
-
- sortOrReverse(int) - Method in class org.jmol.script.ScriptVariable
-
- sources - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Sources files or URLs
- space - Variable in class etomica.action.ActionMinimizeEnergy
-
- space - Variable in class etomica.action.SimulationActionAdapter
-
- space - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- space - Variable in class etomica.AlkaneEH.ConformationMethane
-
- space - Variable in class etomica.AlkaneEH.SpeciesAlkaneEH
-
- space - Variable in class etomica.AlkaneEH.SpeciesMethane
-
- space - Variable in class etomica.association.BiasVolume
-
- space - Variable in class etomica.association.BiasVolumeMolecule
-
- space - Variable in class etomica.association.MCMoveBiasUBMolecule
-
- space - Variable in class etomica.association.MCMoveDimer
-
- space - Variable in class etomica.association.MCMoveDimerRotate
-
- space - Variable in class etomica.association.MCMoveSmer
-
- space - Variable in class etomica.association.MCMoveSmerRotate
-
- space - Variable in class etomica.config.ConfigurationLattice
-
- space - Variable in class etomica.config.ConformationChain
-
- space - Variable in class etomica.config.ConformationChainLinear
-
- space - Variable in class etomica.config.ConformationLinear
-
- space - Variable in class etomica.config.ConformationWater
-
- space - Variable in class etomica.conjugategradient.DerivativeEnergyFunction.MyAgentSource
-
- space - Variable in class etomica.conjugategradient.FiniteDifferenceDerivativeCG.MyAgentSource
-
- space - Variable in class etomica.data.DataProcessorInterfacialTension
-
- space - Variable in class etomica.data.DataSourceAtomDistance
-
- space - Variable in class etomica.data.meter.MeterDihedralAngle
-
- space - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- space - Variable in class etomica.data.meter.MeterRDF
-
- space - Variable in class etomica.data.meter.MeterRDFPC
-
- space - Variable in class etomica.data.meter.MeterStructureFactor
-
- space - Variable in class etomica.data.types.DataTensor.DataInfoTensor
-
- space - Variable in class etomica.data.types.DataTensor.DataInfoTensorFactory
-
- space - Variable in class etomica.data.types.DataVector.DataInfoVector
-
- space - Variable in class etomica.data.types.DataVector.DataInfoVectorFactory
-
- space - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- space - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- space - Variable in class etomica.graphics.DisplayBoxCanvas2D
-
- space - Variable in class etomica.graphics.SimulationGraphic
-
- space - Variable in class etomica.integrator.IntegratorMD
-
- space - Variable in class etomica.integrator.IntegratorMD.VectorSource
-
- space - Variable in class etomica.integrator.mcmove.MCMoveAtom
-
- space - Variable in class etomica.integrator.mcmove.MCMoveBoxSize
-
- space - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- space - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- space - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- space - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- space - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- space - Variable in class etomica.interfacial.ConfigurationLammps
-
- space - Variable in class etomica.interfacial.MeterWallForce
-
- space - Variable in class etomica.lattice.crystal.Primitive
-
- space - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- space - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- space - Variable in class etomica.mappedvirial.MeterMappedU
-
- space - Variable in class etomica.mappedvirial.MeterMappedVirial
-
- space - Variable in class etomica.mappedvirial.MeterMappedVirialV
-
- space - Variable in class etomica.mappedvirial.MeterMeanForce
-
- space - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- space - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- space - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- space - Static variable in class etomica.math.Quaternion
-
- space - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- space - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- space - Variable in class etomica.models.co2.P2CO2Hellmann
-
- space - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- space - Variable in class etomica.models.nitrogen.ConformationNitrogen
-
- space - Variable in class etomica.models.nitrogen.ConformationNitrogenShellModel
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelDecomposed
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMolecule
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequential
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- space - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelDecomposed
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- space - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- space - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- space - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- space - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- space - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- space - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- space - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- space - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- space - Variable in class etomica.models.nitrogen.SpeciesN2
-
- space - Variable in class etomica.models.nitrogen.SpeciesN2B
-
- space - Variable in class etomica.models.nitrogen.SpeciesN2ShellModel
-
- space - Variable in class etomica.models.nitrogen.TestRotationVector
-
- space - Variable in class etomica.models.OPLS.ConformationAceticAcid
-
- space - Variable in class etomica.models.OPLS.SpeciesAceticAcid
-
- space - Variable in class etomica.models.rowley.ConformationEthanol
-
- space - Variable in class etomica.models.rowley.ConformationMethanol
-
- space - Variable in class etomica.models.rowley.SpeciesEthanol
-
- space - Variable in class etomica.models.rowley.SpeciesMethanol
-
- space - Variable in class etomica.models.traPPE.ConformationMethanol
-
- space - Variable in class etomica.models.traPPE.SpeciesMethanol
-
- space - Variable in class etomica.models.water.ConfigurationFileTIP4P
-
- space - Variable in class etomica.models.water.ConformationWater3P
-
- space - Variable in class etomica.models.water.ConformationWaterGCPM
-
- space - Variable in class etomica.models.water.ConformationWaterTIP4P
-
- space - Variable in class etomica.models.water.P2WaterSzalewicz
-
- space - Variable in class etomica.models.water.SpeciesWater3P
-
- space - Variable in class etomica.models.water.SpeciesWater3POriented
-
- space - Variable in class etomica.models.water.SpeciesWater4P
-
- space - Variable in class etomica.models.water.SpeciesWater4PCOM
-
- space - Variable in class etomica.models.water.SpeciesWater4POriented
-
- space - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- space - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- space - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- space - Variable in class etomica.modules.dcvgcmd.ConformationTube
-
- space - Variable in class etomica.modules.materialfracture.P1Tension
-
- space - Variable in class etomica.modules.mu.DataSourceWallPressureMu
-
- space - Variable in class etomica.modules.sam.ConfigurationSAM
-
- space - Variable in class etomica.modules.sam.P1Sinusoidal
-
- space - Variable in class etomica.nbr.cell.BoxAgentSourceCellManager
-
- space - Variable in class etomica.nbr.cell.molecule.BoxAgentSourceCellManagerMolecular
-
- space - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- space - Variable in class etomica.nbr.CriterionSimple
-
- space - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular.NeighborListAgentSourceMolecular
-
- space - Variable in class etomica.nbr.list.molecule.PotentialMasterListMolecular
-
- space - Variable in class etomica.nbr.list.PotentialMasterList.NeighborListAgentSource
-
- space - Variable in class etomica.nbr.list.PotentialMasterList
-
- space - Variable in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- space - Variable in class etomica.normalmode.ConformationHSDimer
-
- space - Variable in class etomica.normalmode.CoordinateDefinition
-
- space - Variable in class etomica.normalmode.HSNPT.ActionSummer
-
- space - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
-
- space - Variable in class etomica.normalmode.MCMovePhaseAngle
-
- space - Variable in class etomica.normalmode.MCMoveWV
-
- space - Variable in class etomica.normalmode.MeterDADB
-
- space - Variable in class etomica.normalmode.MeterSolidProps
-
- space - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- space - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- space - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- space - Variable in class etomica.normalmode.NormalModes2D
-
- space - Variable in class etomica.normalmode.NormalModes3D
-
- space - Variable in class etomica.normalmode.NormalModesMolecular
-
- space - Variable in class etomica.normalmode.NormalModesPotential
-
- space - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- space - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- space - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- space - Variable in class etomica.normalmode.SpeciesHSDimer
-
- space - Variable in class etomica.normalmode.WaveVectorFactorySimple
-
- space - Variable in class etomica.paracetamol.ConformationParacetamol
-
- space - Variable in class etomica.paracetamol.ConformationParacetamolMonoclinic
-
- space - Variable in class etomica.paracetamol.ConformationParacetamolOrthorhombic
-
- space - Variable in class etomica.paracetamol.SpeciesParacetamol
-
- space - Variable in class etomica.parser.ParserLAMMPS.Options
-
- space - Variable in class etomica.potential.EwaldSummation
-
- space - Variable in class etomica.potential.EwaldSumMolecules
-
- space - Variable in class etomica.potential.P2HardWrapper
-
- space - Variable in class etomica.potential.P2NitrogenHellmann
-
- space - Variable in class etomica.potential.P2O2Bartolomei
-
- space - Variable in class etomica.potential.P2SemiclassicalAtomic
-
- space - Variable in class etomica.potential.P2SemiclassicalMolecular
-
- space - Variable in class etomica.potential.P2WaterPotentialsJankowski
-
- space - Variable in class etomica.potential.P3AxilrodTeller
-
- space - Variable in class etomica.potential.P3Induction
-
- space - Variable in class etomica.potential.P3NitrogenHellmannNonAdditive
-
- space - Variable in class etomica.potential.Potential
-
- space - Variable in class etomica.potential.PotentialCalculationPressureTensor
-
- space - Variable in class etomica.potential.PotentialMolecular
-
- space - Variable in class etomica.simulation.Simulation
-
- space - Variable in class etomica.space.Boundary
-
- Space - Class in etomica.space
-
Superclass for all Space instances.
- Space() - Constructor for class etomica.space.Space
-
- space - Variable in class etomica.species.SpeciesOriented
-
- space - Variable in class etomica.species.SpeciesSpheres
-
- space - Variable in class etomica.species.SpeciesSpheresCustom
-
- space - Variable in class etomica.species.SpeciesSpheresHetero
-
- space - Variable in class etomica.species.SpeciesSpheresMono
-
- space - Variable in class etomica.surfacetension.SurfaceTensionMapped
-
- space - Variable in class etomica.virial.BoxCluster
-
- space - Variable in class etomica.virial.ClusterCoupledFlipped
-
- space - Variable in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- space - Variable in class etomica.virial.ClusterCoupledFlippedPartial
-
- space - Variable in class etomica.virial.ConfigurationCluster
-
- space - Variable in class etomica.virial.Conformation7SiteRigidSF6
-
- space - Variable in class etomica.virial.ConformationAnthracene3site
-
- space - Variable in class etomica.virial.ConformationAnthraceneTraPPE
-
- space - Variable in class etomica.virial.ConformationCO2
-
- space - Variable in class etomica.virial.ConformationMethane
-
- space - Variable in class etomica.virial.ConformationNaphthaleneTraPPE
-
- space - Variable in class etomica.virial.ConformationPh3site
-
- space - Variable in class etomica.virial.ConformationPhenanthreneTraPPE
-
- space - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- space - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- space - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- space - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- space - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- space - Variable in class etomica.virial.MCMoveClusterRingScale
-
- space - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- space - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- space - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- space - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- space - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- space - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- space - Variable in class etomica.virial.Species7SiteRigidSF6
-
- space - Variable in class etomica.virial.SpeciesAnthracene3site464
-
- space - Variable in class etomica.virial.SpeciesAnthracene3site545
-
- space - Variable in class etomica.virial.SpeciesFactorySiepmannSpheres
-
- space - Variable in class etomica.virial.SpeciesFactorySpheres2
-
- space - Variable in class etomica.virial.SpeciesMethane
-
- space - Variable in class etomica.virial.SpeciesPh3site464
-
- space - Variable in class etomica.virial.SpeciesPh3site545
-
- space - Variable in class etomica.virial.SpeciesTraPPEAnthracene
-
- space - Variable in class etomica.virial.SpeciesTraPPECO2
-
- space - Variable in class etomica.virial.SpeciesTraPPENaphthalene
-
- space - Variable in class etomica.virial.SpeciesTraPPEPhenanthrene
-
- Space1D - Class in etomica.space1d
-
Factory and methods appropriate to a 1-dimensional space.
- Space2D - Class in etomica.space2d
-
Factory and methods appropriate to a 2-dimensional space.
- Space3D - Class in etomica.space3d
-
Factory and methods appropriate to a 3-dimensional space.
- spacefill - Static variable in class org.jmol.script.Token
-
- SpaceLattice - Interface in etomica.lattice
-
Marker interface indicating that AbstractLattice.site(int[]) returns an
IVector instance.
- spanningVectors - Variable in class org.jmol.util.MeshSurface
-
- spec_alternate - Static variable in class org.jmol.script.Token
-
- spec_atom - Static variable in class org.jmol.script.Token
-
- spec_chain - Static variable in class org.jmol.script.Token
-
- spec_model - Static variable in class org.jmol.script.Token
-
- spec_name_pattern - Static variable in class org.jmol.script.Token
-
- spec_resid - Static variable in class org.jmol.script.Token
-
- spec_seqcode - Static variable in class org.jmol.script.Token
-
- spec_seqcode_range - Static variable in class org.jmol.script.Token
-
- SPECIAL_COLIX_MAX - Static variable in class org.jmol.util.Colix
-
- SpecialFunctions - Class in etomica.math
-
Static-method library of various functions
- specialposition - Static variable in class org.jmol.script.Token
-
- specialRef - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
-
- species - Variable in class etomica.AlkaneEH.DHS_NVT
-
- species - Variable in class etomica.AlkaneEH.DLJ_NVT_1site
-
- species - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- species - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- species - Variable in class etomica.association.TestLJAssociationMC3D_NPT
-
- species - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- species - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld
-
- species - Variable in class etomica.atom.AtomSourceRandomSpecies
-
- species - Variable in class etomica.atom.AtomType
-
- species - Variable in class etomica.box.BoxMoleculeCountEvent
-
- species - Variable in class etomica.config.ConfigurationZincblende
-
- species - Variable in class etomica.data.meter.MeterProfileByAtoms
-
- species - Variable in class etomica.data.meter.MeterProfileByVolume
-
- species - Variable in class etomica.densityofstate.DensityOfState
-
- species - Variable in class etomica.densityofstate.DensityOfStatesPolynomial
-
- species - Variable in class etomica.dielectric.DHS_NVT
-
- species - Variable in class etomica.dielectric.DLJ_NVT_1site
-
- species - Variable in class etomica.dielectric.TIP4P_NVT
-
- species - Variable in class etomica.dimer.PotentialMasterListDimer
-
- species - Variable in class etomica.freeenergy.npath.SimFe
-
- species - Variable in class etomica.freeenergy.npath.SimIdealGas
-
- species - Variable in class etomica.freeenergy.npath.SimLattice
-
- species - Variable in class etomica.freeenergy.npath.SimLJ
-
- species - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic
-
- species - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref
-
- species - Variable in class etomica.graphics.DeviceNSelector
-
- species - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- species - Variable in class etomica.interfacial.ConfigurationLammps
-
- species - Variable in class etomica.interfacial.FixedWall
-
- species - Variable in class etomica.interfacial.WriteConfigurationInterfacial
-
- species - Variable in class etomica.liquidLJ.LjMC3D
-
- species - Variable in class etomica.liquidLJ.LjMd3D
-
- species - Variable in class etomica.mappedRdf.MappedRdf
-
- species - Variable in class etomica.mappedvirial.MappedU
-
- species - Variable in class etomica.mappedvirial.MappedVirialLJ
-
- species - Variable in class etomica.mappedvirial.MappedVirialLJVGr
-
- species - Variable in class etomica.metastable.LJmuVT
-
- species - Variable in class etomica.metastable.LJNPT
-
- species - Variable in class etomica.metastable.LJNVT
-
- species - Variable in class etomica.models.clathrates.ClathrateHarmonicFE
-
- species - Variable in class etomica.models.clathrates.MinimizationTIP4P
-
- species - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2
-
- species - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- species - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- species - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- species - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- species - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModel
-
- species - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameter
-
- species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterFromFile
-
- species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenLatticeParameterLSFromFile
-
- species - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- species - Variable in class etomica.models.nitrogen.MinimizeGammaNitrogenLatticeParameter
-
- species - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP
-
- species - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- species - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- species - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- species - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- species - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- species - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel
-
- species - Variable in class etomica.models.nitrogen.SimulationAlphaNitrogenModel
-
- species - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModel
-
- species - Variable in class etomica.models.nitrogen.SimulationBetaNitrogenModelTest
-
- species - Variable in class etomica.models.nitrogen.SimulationGammaNitrogenModel
-
- species - Variable in class etomica.models.rowley.DimerApproach
-
- species - Variable in class etomica.models.water.TestEwaldTIP4PWater
-
- species - Variable in class etomica.modifier.ModifierNMolecule
-
- species - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- species - Variable in class etomica.modules.chainequilibrium.MeterConversion
-
- species - Variable in class etomica.modules.colloid.ColloidSim
-
- species - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- species - Variable in class etomica.modules.crystalviewer.CrystalViewer
-
- species - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- species - Variable in class etomica.modules.droplet.Droplet
-
- species - Variable in class etomica.modules.droplet.DropletAtomic
-
- species - Variable in class etomica.modules.ensembles.LJMC
-
- species - Variable in class etomica.modules.entropylottery.EntropyLottery
-
- species - Variable in class etomica.modules.insertion.Insertion
-
- species - Variable in class etomica.modules.interfacial.InterfacialSW
-
- species - Variable in class etomica.modules.ljmd.Ljmd
-
- species - Variable in class etomica.modules.materialfracture.MaterialFracture
-
- species - Variable in class etomica.modules.mu.MeterDensitySides
-
- species - Variable in class etomica.modules.mu.MuGraphic.ModifierAtomDiameter
-
- species - Variable in class etomica.modules.multiharmonic.mbar.MultiharmonicMC
-
- species - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicMC
-
- species - Variable in class etomica.modules.multiharmonic.umbrella.MultiharmonicMC
-
- species - Variable in class etomica.modules.pistoncylinder.PistonCylinder
-
- species - Variable in class etomica.modules.render.RenderMD
-
The single hard-sphere species.
- species - Variable in class etomica.modules.rheology.SimulationRheology
-
- species - Variable in class etomica.modules.rosmosis.MeterFlux
-
- species - Variable in class etomica.modules.rosmosis.P1Tether
-
- species - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- species - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- species - Variable in class etomica.modules.sam.MeterTilt
-
- species - Variable in class etomica.modules.sam.Sam
-
- species - Variable in class etomica.modules.swmd.Swmd
-
- species - Variable in class etomica.modules.vle.VLESim
-
- species - Variable in class etomica.molecule.iterator.MoleculeIteratorAll
-
- species - Variable in class etomica.molecule.Molecule
-
- species - Variable in class etomica.molecule.MoleculeToMoleculeListSpecies
-
- species - Variable in class etomica.normalmode.DeviceCellNum3DSlider
-
- species - Variable in class etomica.normalmode.DeviceCellNumXYSlider
-
- species - Variable in class etomica.normalmode.HSDimerNPT
-
- species - Variable in class etomica.normalmode.HSNPT
-
- species - Variable in class etomica.normalmode.HTTPSoftSphereSim
-
- species - Variable in class etomica.normalmode.LJVacancyMin
-
- species - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- species - Variable in class etomica.normalmode.MeterDDP
-
- species - Variable in class etomica.normalmode.MeterDP
-
- species - Variable in class etomica.normalmode.MeterPlaneSlip
-
- species - Variable in class etomica.normalmode.MeterTargetTP
-
- species - Variable in class etomica.normalmode.MeterTilt
-
- species - Variable in class etomica.normalmode.MeterTiltHistogram
-
- species - Variable in class etomica.normalmode.MeterTiltRotation
-
- species - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- species - Variable in class etomica.normalmode.MeterTiltRotationStdev
-
- species - Variable in class etomica.normalmode.ModifierCells3D
-
- species - Variable in class etomica.normalmode.ModifierXCells2D
-
- species - Variable in class etomica.normalmode.ModifierYCells2D
-
- species - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- species - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- species - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- species - Variable in class etomica.normalmode.NormalModesMolecular
-
- species - Variable in class etomica.normalmode.SimBennet
-
- species - Variable in class etomica.normalmode.SimFluidSoftSphere
-
- species - Variable in class etomica.normalmode.SimHarmonic
-
- species - Variable in class etomica.normalmode.SimHarmonicUmbrella
-
- species - Variable in class etomica.normalmode.SimHSMDVacancy
-
- species - Variable in class etomica.normalmode.SimLJHTTISuper
-
- species - Variable in class etomica.normalmode.SimLJHTTISuperHCP
-
- species - Variable in class etomica.normalmode.SimLJVacancy
-
- species - Variable in class etomica.normalmode.SimTargetUmbrella
-
- species - Variable in class etomica.normalmode.SimUmbrella
-
- species - Variable in class etomica.normalmode.SimUmbrellaSoftSphere
-
- species - Variable in class etomica.paracetamol.MCParacetamolMonoclinicDLMULTI
-
- species - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicDLMULTI
-
- species - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonic
-
- species - Variable in class etomica.paracetamol.MCParacetamolOrthorhombicMoveHarmonicStep
-
- species - Variable in class etomica.paracetamol.MDParacetamolMonoclinic
-
The single soft-sphere species.
- species - Variable in class etomica.paracetamol.MDParacetamolOrthorhombic
-
The single soft-sphere species.
- species - Variable in class etomica.parser.ParserLAMMPS.Stuff
-
- species - Variable in class etomica.simulation.prototypes.ChainHSMD3D
-
- species - Variable in class etomica.simulation.prototypes.GEMCWithRotation
-
- species - Variable in class etomica.simulation.prototypes.HSMC2D
-
- species - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- species - Variable in class etomica.simulation.prototypes.HSMD3D
-
The single hard-sphere species.
- species - Variable in class etomica.simulation.prototypes.HSMD3DNoNbr
-
- species - Variable in class etomica.simulation.prototypes.LJMD2D
-
- species - Variable in class etomica.simulation.prototypes.LJMD3D
-
- species - Variable in class etomica.simulation.prototypes.SoftSphere3d
-
- species - Variable in class etomica.simulation.prototypes.SWMD2D
-
- species - Variable in class etomica.simulation.prototypes.SWMD3D
-
- species() - Method in class etomica.simulation.Simulation
-
Convenience method to return the first (and often only) ISpecies
in the simulation.
- Species - Class in etomica.species
-
Type for atom that is a group of other atoms, and for which its node is an instance of AtomTreeNodeGroup.
- Species() - Constructor for class etomica.species.Species
-
- species - Variable in class etomica.surfacetension.LJMC
-
- species - Variable in class etomica.tests.TestHSMD3D
-
- species - Variable in class etomica.tests.TestLJGCMC3D
-
- species - Variable in class etomica.tests.TestLJMC3D
-
- species - Variable in class etomica.thermointegration.LjMc3D
-
- species - Variable in class etomica.threaded.atom.LJMD3DThreaded
-
- species - Variable in class etomica.threaded.domain.LJMD3DThreaded
-
- species - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- species - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- species - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- species - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- species - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- species - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- species - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- species - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- species - Variable in class etomica.virial.simulations.SimulationVirial
-
- species - Variable in class etomica.virial.simulations.SimulationVirialMultiOverlap
-
- species - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- species - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- species - Variable in class etomica.yukawa.TestHC2YukawaMC3D
-
- species - Variable in class etomica.yukawa.TestYukawaMC3D
-
- species - Variable in class etomica.yukawa.TestYukawaMD3D
-
- species - Variable in class etomica.zeolite.ZeoliteSimulation
-
The single hard-sphere species.
- species1 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- species1 - Variable in class etomica.normalmode.nptdemo.HSNPT2DSim
-
- species1 - Variable in class etomica.simulation.prototypes.HSMD2D
-
- SPECIES1_INDEX - Static variable in class etomica.util.Debug
-
- species2 - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- species2 - Variable in class etomica.simulation.prototypes.HSMC2D
-
- species2 - Variable in class etomica.simulation.prototypes.HSMD2D
-
- species2 - Variable in class etomica.tests.TestHSMD3D
-
- SPECIES2_INDEX - Static variable in class etomica.util.Debug
-
- Species7SiteRigidSF6 - Class in etomica.virial
-
Species SF6, 7 sites, LJ, rigid, no partial charge
Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study
- Species7SiteRigidSF6(Space) - Constructor for class etomica.virial.Species7SiteRigidSF6
-
- Species7SiteRigidSF6(Space, boolean) - Constructor for class etomica.virial.Species7SiteRigidSF6
-
- speciesA - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- speciesA - Variable in class etomica.modules.adsorption.Adsorption
-
- speciesA - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- speciesA - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- speciesA - Variable in class etomica.modules.mu.Mu
-
- speciesA - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- speciesA - Variable in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- speciesA - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- SpeciesAceticAcid - Class in etomica.models.OPLS
-
Species for OPLS acetic acid
- SpeciesAceticAcid(Space) - Constructor for class etomica.models.OPLS.SpeciesAceticAcid
-
- speciesAdded(ISpecies) - Method in class etomica.simulation.SimulationEventManager
-
- speciesAgentManager - Variable in class etomica.nbr.molecule.PotentialMasterNbrMolecular
-
- SpeciesAgentManager<E> - Class in etomica.species
-
AtomTypeAgentManager acts on behalf of client classes (an AgentSource) to
manage agents in every AtomType in a box.
- SpeciesAgentManager(SpeciesAgentManager.AgentSource<E>, Simulation) - Constructor for class etomica.species.SpeciesAgentManager
-
- SpeciesAgentManager.AgentSource<E> - Interface in etomica.species
-
Interface for an object that wants an agent associated with each
AtomType in a Simulation.
- SpeciesAlkane - Class in etomica.virial
-
- SpeciesAlkane(Space, int) - Constructor for class etomica.virial.SpeciesAlkane
-
- SpeciesAlkane(Space, int, ElementSimple, ElementSimple) - Constructor for class etomica.virial.SpeciesAlkane
-
- speciesAlkaneEH - Variable in class etomica.AlkaneEH.ConformationAlkaneEH
-
- SpeciesAlkaneEH - Class in etomica.AlkaneEH
-
Species for TraPPE-Explicit hydrogen,Siepmann
- SpeciesAlkaneEH(Space, int) - Constructor for class etomica.AlkaneEH.SpeciesAlkaneEH
-
- SpeciesAlkaneThiol - Class in etomica.modules.sam
-
- SpeciesAlkaneThiol(Space, int) - Constructor for class etomica.modules.sam.SpeciesAlkaneThiol
-
- SpeciesAnthracene3site464 - Class in etomica.virial
-
Species Anthracene molecule
rigid , LJ potential, no charge, this model is very similar to 3site 545 model, only the weight of the sites are different
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
* @author shu
March, 7, 2011
- SpeciesAnthracene3site464(Space) - Constructor for class etomica.virial.SpeciesAnthracene3site464
-
- SpeciesAnthracene3site464(Space, boolean) - Constructor for class etomica.virial.SpeciesAnthracene3site464
-
- SpeciesAnthracene3site545 - Class in etomica.virial
-
Species Anthracene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
* @author shu
March, 7, 2011
- SpeciesAnthracene3site545(Space) - Constructor for class etomica.virial.SpeciesAnthracene3site545
-
- SpeciesAnthracene3site545(Space, boolean) - Constructor for class etomica.virial.SpeciesAnthracene3site545
-
- speciesB - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- speciesB - Variable in class etomica.modules.adsorption.Adsorption
-
- speciesB - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- speciesB - Variable in class etomica.modules.chainequilibrium.FreeRadicalPolymerizationSim
-
- speciesB - Variable in class etomica.modules.mu.Mu
-
- speciesB - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- speciesB - Variable in class etomica.normalmode.CoordinateDefinitionLeafSuperBox
-
- speciesB - Variable in class etomica.normalmode.SimCalcSSoftSphereFCCSuperBox
-
- speciesBottomWall - Variable in class etomica.interfacial.LJMC
-
- speciesBottomWall - Variable in class etomica.interfacial.LJMD
-
- speciesC - Variable in class etomica.modules.catalysis.Catalysis
-
- speciesC - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- speciesC - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- speciesC - Variable in class etomica.modules.catalysis.MeterDensityCO
-
- speciesC - Variable in class etomica.modules.catalysis.MeterDensityCO2
-
- speciesCH4 - Variable in class etomica.AlkaneEH.CH4NVT
-
- speciesChlorine - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- speciesColloid - Variable in class etomica.modules.colloid.ColloidSim
-
- speciesColloid - Variable in class etomica.modules.colloid.ConfigurationColloid
-
- speciesColloid - Variable in class etomica.modules.colloid.NeighborListManagerColloid
-
- speciesEthanol - Static variable in class etomica.models.rowley.DimerApproach
-
- SpeciesEthanol - Class in etomica.models.rowley
-
Species for ethanol with satellite site (Rowley et al 2006).
- SpeciesEthanol(Space, boolean) - Constructor for class etomica.models.rowley.SpeciesEthanol
-
- SpeciesFactory - Interface in etomica.virial
-
- SpeciesFactoryEthanol - Class in etomica.models.rowley
-
SpeciesFactory that makes ethanol.
- SpeciesFactoryEthanol(boolean) - Constructor for class etomica.models.rowley.SpeciesFactoryEthanol
-
- SpeciesFactoryMethanol - Class in etomica.models.rowley
-
SpeciesFactory that makes methanol.
- SpeciesFactoryMethanol(boolean) - Constructor for class etomica.models.rowley.SpeciesFactoryMethanol
-
- SpeciesFactoryMethanol - Class in etomica.models.traPPE
-
SpeciesFactory that makes methanol.
- SpeciesFactoryMethanol() - Constructor for class etomica.models.traPPE.SpeciesFactoryMethanol
-
- SpeciesFactoryOrientedSpheres - Class in etomica.virial
-
SpeciesFactory that makes SpeciesSpheresMono
- SpeciesFactoryOrientedSpheres() - Constructor for class etomica.virial.SpeciesFactoryOrientedSpheres
-
- SpeciesFactorySiepmannSpheres - Class in etomica.virial
-
SpeciesFactory that makes Siepmann's alkane model.
- SpeciesFactorySiepmannSpheres(Space, int) - Constructor for class etomica.virial.SpeciesFactorySiepmannSpheres
-
- SpeciesFactorySiepmannSpheres(Space, int, double, double) - Constructor for class etomica.virial.SpeciesFactorySiepmannSpheres
-
- SpeciesFactorySpheres - Class in etomica.virial
-
SpeciesFactory that makes SpeciesSpheresMono
- SpeciesFactorySpheres() - Constructor for class etomica.virial.SpeciesFactorySpheres
-
- SpeciesFactorySpheres2 - Class in etomica.virial
-
- SpeciesFactorySpheres2(Space, int, ElementSimple, ElementSimple) - Constructor for class etomica.virial.SpeciesFactorySpheres2
-
- SpeciesFactorySpheres2(Space, int, ElementSimple, ElementSimple, double, double) - Constructor for class etomica.virial.SpeciesFactorySpheres2
-
- SpeciesFactoryTangentSpheres - Class in etomica.virial
-
SpeciesFactory that makes a tangent sphere species.
- SpeciesFactoryTangentSpheres(int, IConformation) - Constructor for class etomica.virial.SpeciesFactoryTangentSpheres
-
- SpeciesFactoryWater3P - Class in etomica.virial
-
SpeciesFactory that makes SpeciesWater
- SpeciesFactoryWater3P() - Constructor for class etomica.virial.SpeciesFactoryWater3P
-
- SpeciesFactoryWater4P - Class in etomica.virial
-
SpeciesFactory that makes SpeciesWater
- SpeciesFactoryWater4P(IConformation) - Constructor for class etomica.virial.SpeciesFactoryWater4P
-
- SpeciesFactoryWaterGCPM - Class in etomica.virial
-
SpeciesFactory that makes SpeciesWater
- SpeciesFactoryWaterGCPM() - Constructor for class etomica.virial.SpeciesFactoryWaterGCPM
-
- speciesFluid - Variable in class etomica.interfacial.LJMC
-
- speciesFluid - Variable in class etomica.interfacial.LJMD
-
- speciesGhost - Variable in class etomica.modules.insertion.Insertion
-
- SpeciesHexane - Class in etomica.models.hexane
-
Species used to create hexane molecules per Dr.
- SpeciesHexane(Space) - Constructor for class etomica.models.hexane.SpeciesHexane
-
- SpeciesHSDimer - Class in etomica.normalmode
-
Species hard-sphere dimer molecule
- SpeciesHSDimer(Space) - Constructor for class etomica.normalmode.SpeciesHSDimer
-
- SpeciesHSDimer(Space, boolean, double) - Constructor for class etomica.normalmode.SpeciesHSDimer
-
- speciesIndex - Variable in class etomica.virial.GUI.components.CollectionPotentialAtomicUnlike
-
- speciesIndex - Variable in class etomica.virial.GUI.components.CollectionPotentialMolecularUnlike
-
- speciesIndexChanged(ISpecies, int) - Method in class etomica.simulation.SimulationEventManager
-
- speciesInitiator - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
-
- speciesMade - Variable in class etomica.chem.models.ModelChain
-
- speciesMaxIndexChanged(int) - Method in class etomica.simulation.SimulationEventManager
-
- speciesMembrane - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- speciesMembrane - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- speciesMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- speciesMembrane - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- SpeciesMethane - Class in etomica.AlkaneEH
-
Species for methane with explicit hydrogen
Bond angle = 109.5 -- not exactly, conformation is changed!!!
- SpeciesMethane(Space) - Constructor for class etomica.AlkaneEH.SpeciesMethane
-
- SpeciesMethane(Space, boolean) - Constructor for class etomica.AlkaneEH.SpeciesMethane
-
- SpeciesMethane - Class in etomica.virial
-
Species for methane with explicit hydrogen
Bond angle = 109.5
- SpeciesMethane(Space) - Constructor for class etomica.virial.SpeciesMethane
-
- SpeciesMethane(Space, boolean) - Constructor for class etomica.virial.SpeciesMethane
-
- speciesMethanol - Static variable in class etomica.models.rowley.DimerApproach
-
- SpeciesMethanol - Class in etomica.models.rowley
-
Species for methanol with satellite site (Rowley et al 2006).
- SpeciesMethanol(Space, boolean) - Constructor for class etomica.models.rowley.SpeciesMethanol
-
- SpeciesMethanol - Class in etomica.models.traPPE
-
Species for methanol with satellite site (Rowley et al 2006).
- SpeciesMethanol(Space) - Constructor for class etomica.models.traPPE.SpeciesMethanol
-
- speciesMolecules - Variable in class etomica.modules.sam.ConfigurationSAM
-
- speciesMonomer - Variable in class etomica.modules.chainequilibrium.ConfigurationLatticeFreeRadical
-
- speciesMonomer - Variable in class etomica.modules.colloid.NeighborListManagerColloid
-
- SpeciesN2 - Class in etomica.models.nitrogen
-
Species nitrogen molecule
with 4-points charges
- SpeciesN2(Space) - Constructor for class etomica.models.nitrogen.SpeciesN2
-
- SpeciesN2(Space, boolean) - Constructor for class etomica.models.nitrogen.SpeciesN2
-
- SpeciesN2B - Class in etomica.models.nitrogen
-
Species nitrogen molecule
with 4-points charges
- SpeciesN2B(Space) - Constructor for class etomica.models.nitrogen.SpeciesN2B
-
- SpeciesN2B(Space, boolean) - Constructor for class etomica.models.nitrogen.SpeciesN2B
-
- SpeciesN2ShellModel - Class in etomica.models.nitrogen
-
Species nitrogen molecule (shell model)
Reference: Fabianski R.
- SpeciesN2ShellModel(Space) - Constructor for class etomica.models.nitrogen.SpeciesN2ShellModel
-
- SpeciesN2ShellModel(Space, boolean) - Constructor for class etomica.models.nitrogen.SpeciesN2ShellModel
-
- speciesO - Variable in class etomica.modules.catalysis.Catalysis
-
- speciesO - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- speciesO - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- speciesO - Variable in class etomica.modules.catalysis.MeterDensityO2
-
- SpeciesOriented - Class in etomica.species
-
Atom type for a rigid molecule with an orientation and (therefore) a moment
of inertia.
- SpeciesOriented(Space) - Constructor for class etomica.species.SpeciesOriented
-
- SpeciesParacetamol - Class in etomica.paracetamol
-
- SpeciesParacetamol(Space, boolean) - Constructor for class etomica.paracetamol.SpeciesParacetamol
-
- SpeciesPh3site464 - Class in etomica.virial
-
Species Phenanthrene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site, 464 model
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
- SpeciesPh3site464(Space) - Constructor for class etomica.virial.SpeciesPh3site464
-
- SpeciesPh3site464(Space, boolean) - Constructor for class etomica.virial.SpeciesPh3site464
-
- SpeciesPh3site545 - Class in etomica.virial
-
Species Phenanthrene molecule
rigid , LJ potential, no charge, 3 site model.each benzene ring is a site
reference: Iwai, monte carlo sim of Naphthalene, phenathlene,anthracene in SCF 1998
- SpeciesPh3site545(Space) - Constructor for class etomica.virial.SpeciesPh3site545
-
- SpeciesPh3site545(Space, boolean) - Constructor for class etomica.virial.SpeciesPh3site545
-
- SpeciesPolyhedron - Class in etomica.species
-
Species in which molecules are made of a single atom of type SpheroPolyhedron
- SpeciesPolyhedron(Simulation, Space, List<Vector>, double) - Constructor for class etomica.species.SpeciesPolyhedron
-
- SpeciesPolyhedron(Space, List<Vector>, double, IElement) - Constructor for class etomica.species.SpeciesPolyhedron
-
- speciesRemoved(ISpecies) - Method in class etomica.simulation.SimulationEventManager
-
- speciesSodium - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- speciesSolute - Variable in class etomica.modules.osmosis.OsmosisSim
-
- speciesSolute - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- speciesSolute - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- speciesSolute1 - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- speciesSolute2 - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- speciesSolvent - Variable in class etomica.modules.osmosis.OsmosisSim
-
- speciesSolvent - Variable in class etomica.modules.rosmosis.ConfigurationMembrane
-
- speciesSolvent - Variable in class etomica.modules.rosmosis.ConfigurationMembraneWater
-
- speciesSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosis
-
- speciesSolvent - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- speciesSpheres - Variable in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
-
- SpeciesSpheres - Class in etomica.species
-
Species in which molecules are made of arbitrary number of spheres,
with each sphere having the same mass and size (same type).
- SpeciesSpheres(Simulation, Space) - Constructor for class etomica.species.SpeciesSpheres
-
- SpeciesSpheres(Simulation, Space, int) - Constructor for class etomica.species.SpeciesSpheres
-
- SpeciesSpheres(Space, int, IElement) - Constructor for class etomica.species.SpeciesSpheres
-
- SpeciesSpheres(int, IElement, IConformation, Space) - Constructor for class etomica.species.SpeciesSpheres
-
- SpeciesSpheres(Space, int, AtomType, IConformation) - Constructor for class etomica.species.SpeciesSpheres
-
- SpeciesSpheresCustom - Class in etomica.species
-
Species in which molecules are made of arbitrary number of spheres,
each of a specified type.
- SpeciesSpheresCustom(Simulation, Space) - Constructor for class etomica.species.SpeciesSpheresCustom
-
Constructs instance with 0 components and total number of children
equal to 1.
- SpeciesSpheresCustom(Simulation, Space, int) - Constructor for class etomica.species.SpeciesSpheresCustom
-
Constructs instance with the given number of atom types.
- SpeciesSpheresCustom(Space, IElement[]) - Constructor for class etomica.species.SpeciesSpheresCustom
-
Constructs instance with the given elements.
- SpeciesSpheresCustom(Space, AtomType[]) - Constructor for class etomica.species.SpeciesSpheresCustom
-
Constructs instance with the given atom types.
- SpeciesSpheresHetero - Class in etomica.species
-
Species in which molecules are made of arbitrary number of atoms, with each
atom have a given atom type.
- SpeciesSpheresHetero(Simulation, Space) - Constructor for class etomica.species.SpeciesSpheresHetero
-
Constructs instance with 0 components and total number of children
equal to 1.
- SpeciesSpheresHetero(Simulation, Space, int) - Constructor for class etomica.species.SpeciesSpheresHetero
-
Constructs instance with the given number of atom types.
- SpeciesSpheresHetero(Space, IElement[]) - Constructor for class etomica.species.SpeciesSpheresHetero
-
Constructs instance with the given elements.
- SpeciesSpheresHetero(Space, AtomType[]) - Constructor for class etomica.species.SpeciesSpheresHetero
-
Constructs instance with the given atom types.
- SpeciesSpheresMono - Class in etomica.species
-
Species in which molecules are each made of a single spherical atom.
- SpeciesSpheresMono(Simulation, Space) - Constructor for class etomica.species.SpeciesSpheresMono
-
Constructs instance with a default element
- SpeciesSpheresMono(Space, IElement) - Constructor for class etomica.species.SpeciesSpheresMono
-
- SpeciesSpheresMono(Space, AtomType) - Constructor for class etomica.species.SpeciesSpheresMono
-
- SpeciesSpheresRotating - Class in etomica.species
-
Species in which molecules are made of a single atom of type OrientedSphere
- SpeciesSpheresRotating(Simulation, Space) - Constructor for class etomica.species.SpeciesSpheresRotating
-
- SpeciesSpheresRotating(Space, IElement) - Constructor for class etomica.species.SpeciesSpheresRotating
-
- SpeciesSpheresRotatingMolecule - Class in etomica.species
-
Species in which molecules are made of a single atom.
- SpeciesSpheresRotatingMolecule(Simulation, Space) - Constructor for class etomica.species.SpeciesSpheresRotatingMolecule
-
- SpeciesSpheresRotatingMolecule(Simulation, Space, Vector) - Constructor for class etomica.species.SpeciesSpheresRotatingMolecule
-
- SpeciesSpheresRotatingMolecule(Space, AtomType, Vector) - Constructor for class etomica.species.SpeciesSpheresRotatingMolecule
-
- speciesSurface - Variable in class etomica.modules.catalysis.Catalysis
-
- speciesSurface - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- speciesSurface - Variable in class etomica.modules.catalysis.InteractionTracker
-
- speciesSurface - Variable in class etomica.modules.sam.ConfigurationSAM
-
- speciesSurface - Variable in class etomica.modules.sam.Sam
-
- speciesTopWall - Variable in class etomica.interfacial.LJMC
-
- speciesTopWall - Variable in class etomica.interfacial.LJMD
-
- SpeciesTraPPEAnthracene - Class in etomica.virial
-
Species Anthracene molecule
this is for TraPPE, the Anthracene is rigid , LJ potential, 10 interaction site
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
modified from Species Anthracene molecule class
- SpeciesTraPPEAnthracene(Space) - Constructor for class etomica.virial.SpeciesTraPPEAnthracene
-
- SpeciesTraPPEAnthracene(Space, boolean) - Constructor for class etomica.virial.SpeciesTraPPEAnthracene
-
- SpeciesTraPPECO2 - Class in etomica.virial
-
Species CO2 molecule
this is for TraPPE, the CO2 is rigid , LJ potential + QQ
- SpeciesTraPPECO2(Space) - Constructor for class etomica.virial.SpeciesTraPPECO2
-
- SpeciesTraPPECO2(Space, boolean) - Constructor for class etomica.virial.SpeciesTraPPECO2
-
- SpeciesTraPPENaphthalene - Class in etomica.virial
-
Species Naphthalene molecule
this is for TraPPE, the Naphthalene is rigid , LJ potential
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
- SpeciesTraPPENaphthalene(Space) - Constructor for class etomica.virial.SpeciesTraPPENaphthalene
-
- SpeciesTraPPENaphthalene(Space, boolean) - Constructor for class etomica.virial.SpeciesTraPPENaphthalene
-
- SpeciesTraPPEPhenanthrene - Class in etomica.virial
-
Species Phenanthrene molecule
this is for TraPPE, the Phenanthrene is rigid , LJ potential
reference: TraPPE 4, UA description of linear and branched alkanes and alkylbenzenes, Siepmann
modified from species of phenanthrene C14H10
- SpeciesTraPPEPhenanthrene(Space) - Constructor for class etomica.virial.SpeciesTraPPEPhenanthrene
-
- SpeciesTraPPEPhenanthrene(Space, boolean) - Constructor for class etomica.virial.SpeciesTraPPEPhenanthrene
-
- speciesTube - Variable in class etomica.modules.dcvgcmd.ConfigurationLatticeTube
-
- speciesTube - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- SpeciesTube - Class in etomica.modules.dcvgcmd
-
- SpeciesTube(int, int, Space) - Constructor for class etomica.modules.dcvgcmd.SpeciesTube
-
- SpeciesWater3P - Class in etomica.models.water
-
Species for 3-point water molecule.
- SpeciesWater3P(Space) - Constructor for class etomica.models.water.SpeciesWater3P
-
- SpeciesWater3P(Space, boolean) - Constructor for class etomica.models.water.SpeciesWater3P
-
- SpeciesWater3POriented - Class in etomica.models.water
-
- SpeciesWater3POriented(Space, boolean) - Constructor for class etomica.models.water.SpeciesWater3POriented
-
- SpeciesWater4P - Class in etomica.models.water
-
Species for 4-point water molecule.
- SpeciesWater4P(Space) - Constructor for class etomica.models.water.SpeciesWater4P
-
- SpeciesWater4P(Space, boolean) - Constructor for class etomica.models.water.SpeciesWater4P
-
- SpeciesWater4PCOM - Class in etomica.models.water
-
Species for 4-point water molecule.
- SpeciesWater4PCOM(Space) - Constructor for class etomica.models.water.SpeciesWater4PCOM
-
- SpeciesWater4PCOM(Space, boolean) - Constructor for class etomica.models.water.SpeciesWater4PCOM
-
- SpeciesWater4POriented - Class in etomica.models.water
-
- SpeciesWater4POriented(Space, boolean) - Constructor for class etomica.models.water.SpeciesWater4POriented
-
- specular - Static variable in class org.jmol.script.Token
-
- specularexponent - Static variable in class org.jmol.script.Token
-
- specularExponent - Static variable in class org.jmol.util.Shader
-
- specularFactor - Static variable in class org.jmol.util.Shader
-
- specularOn - Static variable in class org.jmol.util.Shader
-
- specularpercent - Static variable in class org.jmol.script.Token
-
- specularPercent - Static variable in class org.jmol.util.Shader
-
- specularpower - Static variable in class org.jmol.script.Token
-
- specularPower - Static variable in class org.jmol.util.Shader
-
- Sphere - Class in etomica.math.geometry
-
A sphere in 3D.
- Sphere() - Constructor for class etomica.math.geometry.Sphere
-
Creates sphere with unit radius
- Sphere(double) - Constructor for class etomica.math.geometry.Sphere
-
Creates sphere of the given radius.
- sphere - Static variable in class org.jmol.script.Token
-
- sphereArea(double) - Method in class etomica.space.Space
-
The surface "area" of the "sphere" defined in the D-dimensional space.
- sphereArea(double) - Method in class etomica.space1d.Space1D
-
- sphereArea(double) - Method in class etomica.space2d.Space2D
-
Returns 2 PI r.
- sphereArea(double) - Method in class etomica.space3d.Space3D
-
- sphereMean(Quaternion[], float[], float) - Static method in class org.jmol.util.Quaternion
-
- SphereRenderer - Class in org.jmol.g3d
-
Implements high performance rendering of shaded spheres.
- sphereShadeIndexes - Static variable in class org.jmol.util.Shader
-
- sphereShadingCalculated - Static variable in class org.jmol.util.Shader
-
- sphereShapeCache - Static variable in class org.jmol.util.Shader
-
- sphereVolume(double) - Method in class etomica.space.Space
-
The "volume" of the "sphere" defined in the D-dimensional space.
- sphereVolume(double) - Method in class etomica.space1d.Space1D
-
- sphereVolume(double) - Method in class etomica.space2d.Space2D
-
Returns PI r^2.
- sphereVolume(double) - Method in class etomica.space3d.Space3D
-
- spiffiness - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaChi
-
- spine - Static variable in class org.jmol.script.Token
-
- spinfps - Static variable in class org.jmol.script.Token
-
- spinner - Variable in class etomica.graphics.DeviceSpinner
-
Actual JSpinner
- SpinnerListener() - Constructor for class etomica.graphics.DeviceSpinner.SpinnerListener
-
- spinnerModel - Variable in class etomica.graphics.DeviceSpinner
-
Actual spinner model
- spins - Variable in class etomica.spin.Heisenberg
-
- spinx - Static variable in class org.jmol.script.Token
-
- spiny - Static variable in class org.jmol.script.Token
-
- spinz - Static variable in class org.jmol.script.Token
-
- spline - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- spline(double[], double, double) - Static method in class etomica.potential.P2O2Bartolomei
-
- spline - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- splineC10 - Variable in class etomica.potential.P2QChemInterpolated
-
- splineC6 - Variable in class etomica.potential.P2QChemInterpolated
-
- splineC8 - Variable in class etomica.potential.P2QChemInterpolated
-
- splineRatio - Variable in class etomica.potential.P2QChemInterpolated
-
- splineRc - Variable in class etomica.potential.P2QChemInterpolated
-
- splineUSCF - Variable in class etomica.potential.P2QChemInterpolated
-
- splint(double[], double[], double) - Static method in class etomica.potential.P2O2Bartolomei
-
- Split - Class in etomica.graph.operations
-
- Split() - Constructor for class etomica.graph.operations.Split
-
- split(String, char) - Static method in class org.jmol.util.TextFormat
-
- splitChars(String, String) - Static method in class org.jmol.util.TextFormat
-
proper splitting, even for Java 1.3 -- if the text ends in the run,
no new line is appended.
- SplitGraph - Class in etomica.graph.operations
-
Split a disconnected graph into multiple graphs.
- SplitGraph() - Constructor for class etomica.graph.operations.SplitGraph
-
- splitGrapher - Variable in class etomica.graph.operations.ComponentSubst
-
- SplitOne - Class in etomica.graph.operations
-
Performs the substitution 1=a+b.
- SplitOne() - Constructor for class etomica.graph.operations.SplitOne
-
- SplitOne.SplitOneParameters - Class in etomica.graph.operations
-
- splitOneBC - Variable in class etomica.virial.PYGenerator.IteratorEF
-
- SplitOneBiconnected - Class in etomica.graph.operations
-
Performs the substitution 1=a+b within each biconnected component.
- SplitOneBiconnected() - Constructor for class etomica.graph.operations.SplitOneBiconnected
-
- SplitOneBiconnected.SplitOneParametersBC - Class in etomica.graph.operations
-
- SplitOneParameters(char, char) - Constructor for class etomica.graph.operations.SplitOne.SplitOneParameters
-
- splitOneParameters - Variable in class etomica.virial.PYGenerator.IteratorEF
-
- SplitOneParametersBC(char, char, char) - Constructor for class etomica.graph.operations.SplitOneBiconnected.SplitOneParametersBC
-
- SplitParameters - Class in etomica.graph.operations
-
- SplitParameters(char, char, char) - Constructor for class etomica.graph.operations.SplitParameters
-
- SplitParameters(char, char, char, Property) - Constructor for class etomica.graph.operations.SplitParameters
-
- splitSets(Set<Graph>, int) - Method in class etomica.graph.operations.DecorateWertheim3SiteRho
-
- splitter - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- splitter - Variable in class etomica.overlap.DataOverlap.DataSourceOverlapAvgCollapsingSplit
-
- splitterA - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- splitterB - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC
-
- spring - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- spring - Variable in class etomica.interfacial.P1Wall
-
- spring - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- spring - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
-
- spring - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- spring - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
-
- spring - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- spring - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- springPosition - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- springPosition - Variable in class etomica.interfacial.P1Wall
-
- sprintf(String, ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- sprintf(String, String, Object[]) - Static method in class org.jmol.util.TextFormat
-
sprintf emulation uses (almost) c++ standard string formats 's' string 'i'
or 'd' integer 'f' float/decimal 'p' point3f 'q' quaternion/plane/axisangle
' with added "i" in addition to the insipid "d" (digits?)
- sprintfArray(ScriptVariable[]) - Static method in class org.jmol.script.ScriptVariable
-
sprintf accepts arguments from the format() function
First argument is a format string.
- sqdt - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- sqr() - Method in class etomica.veos.bigdecimal.BigSurd
-
Compute the square.
- sqr() - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Compute the square.
- sqrt() - Method in class etomica.math.Complex
-
Complex square root (doesn't change this complex number).
- Sqrt() - Constructor for class etomica.math.function.Function.Sqrt
-
- sqrt(BigDecimal, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The square root.
- sqrt(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The square root.
- sqrt2 - Variable in class etomica.statmech.HardSphere
-
- sqrt2 - Static variable in class etomica.statmech.HardSphereSolid
-
- sqrt3a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
-
- sqrt3a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
-
- sqrt3ofhalfofthebondlength - Static variable in class etomica.virial.ConformationNaphthaleneTraPPE
-
- sqrtCOtau - Variable in class etomica.models.co2.PNCO2GCPM
-
- sqrtHMsigmas - Variable in class etomica.models.water.PNWaterGCPM
-
- sqrtPI - Variable in class etomica.potential.EwaldSummation
-
- sqrtPiCCtau - Variable in class etomica.models.co2.PNCO2GCPM
-
- sqrtPiCOtau - Variable in class etomica.models.co2.PNCO2GCPM
-
- sqrtPiHMsigmas - Variable in class etomica.models.water.PNWaterGCPM
-
- sqrtPiMMsigmas - Variable in class etomica.models.water.PNWaterGCPM
-
- sqrtSimOmega2 - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- sqrtSimOmega2 - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- sqrtTemperature - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- sqrtWVC - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- sqrtWVC - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- Square - Class in etomica.math.geometry
-
A 2-dimensional geometric square.
- Square(Space) - Constructor for class etomica.math.geometry.Square
-
Constructs a square of unit size.
- Square(Space, double) - Constructor for class etomica.math.geometry.Square
-
Constructs a square with edge length having the given value.
- squared() - Method in interface etomica.space.Vector
-
Returns the square magnitude of this vector, e.g., x^2 + y^2 for D = 2.
- squared() - Method in class etomica.space1d.Vector1D
-
- squared() - Method in class etomica.space2d.Vector2D
-
- squared() - Method in class etomica.space3d.Vector3D
-
- squared() - Method in class etomica.spaceNd.VectorND
-
- sqv - Variable in class etomica.potential.P2SpheroPolyhedron
-
- ss - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- ss - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
-
- ss - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- ss - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- ss - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- ssbond - Static variable in class org.jmol.script.Token
-
- ssbondsbackbone - Static variable in class org.jmol.script.Token
-
- ssInit - Variable in class etomica.math.numerical.AkimaSplineSmootherDy
-
- Standard - Class in etomica.virial.cluster
-
- STANDARD_DEVIATION - Static variable in class etomica.data.AccumulatorAverage
-
- STANDARD_DEVIATION - Static variable in class etomica.data.AccumulatorAverageBlockless
-
- STANDARD_DEVIATION - Static variable in class etomica.data.AccumulatorAverageBlocklessSlim
-
- standardDeviation - Variable in class etomica.data.AccumulatorAverage
-
- standardDeviation - Variable in class etomica.data.AccumulatorAverageBlockless
-
- standardLensPoint - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- standardLevel - Static variable in class org.jmol.util.Geodesic
-
3 levels, 0 through 3
- star - Static variable in class org.jmol.script.Token
-
- start() - Method in class etomica.graph.iterators.ChainedIterator
-
- START - Static variable in class etomica.util.Debug
-
what step of the integrator debugging should start from.
- start - Variable in class g3dsys.images.Line
-
- startAtom - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- startAtom - Variable in class etomica.virial.MCMoveClusterAtomMulti
-
- startAtom0 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
-
- startAtom1 - Variable in class etomica.atom.iterator.ApiIntergroupExchange
-
- startBeadHalfs - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- starter - Variable in class etomica.modules.clustergenerator.MyApplet
-
- Starter() - Constructor for class etomica.modules.clustergenerator.MyApplet.Starter
-
- startMolecule - Variable in class etomica.virial.MCMoveClusterMoleculeMulti
-
- startOrtho - Variable in class etomica.dimer.IntegratorDimerRT
-
- startRotate(float, float) - Method in class etomica.graphics.DisplayCanvas
-
- startRotation(int, int) - Method in class g3dsys.control.G3DSys
-
- startTimer(String) - Static method in class org.jmol.util.Logger
-
- startWithDim(Dimension) - Method in class etomica.units.gui.UnitGraphics
-
- statChoices() - Static method in class etomica.data.AccumulatorAverage
-
- statChoices() - Static method in class etomica.data.AccumulatorAverageBlockless
-
- statChoices() - Static method in class etomica.data.AccumulatorAverageBlocklessSlim
-
- statChoices() - Static method in class etomica.data.AccumulatorAverageCovariance
-
- Statcoulomb - Class in etomica.units
-
The statcoulomb unit of electrical charge, which is the
standard unit of charge in the CGS unit system.
- state(int) - Method in interface etomica.tmmc.MacrostateManager
-
Returns the value of the macrostate variable corresponding to the given index.
- stateChanged(ChangeEvent) - Method in class etomica.graphics.DeviceBox
-
calls doUpdate method.
- stateChanged(ChangeEvent) - Method in class etomica.graphics.DeviceSpinner.SpinnerListener
-
- stateChanged(ChangeEvent) - Method in class etomica.graphics.DisplayTextBox
-
calls doUpdate method.
- stateIndex(Box) - Method in interface etomica.tmmc.MacrostateManager
-
Returns an index identifying the current macrostate occupied by the box.
- stateUpDown - Variable in class etomica.atom.iterator.TripletInnerSequential
-
- StaticConstants - Class in org.jmol.constant
-
- StaticConstants() - Constructor for class org.jmol.constant.StaticConstants
-
- StatisticsMCGraphic - Class in etomica.modules.statistics
-
- StatisticsMCGraphic(LJMC, int) - Constructor for class etomica.modules.statistics.StatisticsMCGraphic
-
- StatisticsMCGraphic.DataProcessorUndo - Class in etomica.modules.statistics
-
- StatisticsMCGraphic.HistoryPlotBits - Class in etomica.modules.statistics
-
- StatisticsMCGraphic.MyFunctionInvertible - Class in etomica.modules.statistics
-
- StatisticsMCGraphic.StatsParams - Class in etomica.modules.statistics
-
- StatsParams() - Constructor for class etomica.modules.statistics.StatisticsMCGraphic.StatsParams
-
- StatType(String, int) - Constructor for class etomica.data.AccumulatorAverage.StatType
-
- StatType(String, int) - Constructor for class etomica.data.AccumulatorAverageBlockless.StatType
-
- StatType(String, int) - Constructor for class etomica.data.AccumulatorAverageBlocklessSlim.StatType
-
- status(byte) - Method in class etomica.graph.traversal.AbstractTraversal
-
- STATUS_ARTICULATION_POINT - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_START_BICOMPONENT - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_START_COMPONENT - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_VISITED_ALL - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_VISITED_BICOMPONENT - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_VISITED_COMPONENT - Static variable in interface etomica.graph.traversal.Traversal
-
- STATUS_VISITED_NODE - Static variable in interface etomica.graph.traversal.Traversal
-
- StatusAction - Class in etomica.server.representations
-
- StatusAction() - Constructor for class etomica.server.representations.StatusAction
-
- StatusAction.Status - Enum in etomica.server.representations
-
- statusreporting - Static variable in class org.jmol.script.Token
-
- stddev - Static variable in class org.jmol.script.Token
-
- stdev - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- stdev - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- STDEV - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- STDEV - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- STDEV2 - Static variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceBias
-
- SteepestDescent - Class in etomica.conjugategradient
-
- SteepestDescent(Matrix, Matrix, Matrix, int) - Constructor for class etomica.conjugategradient.SteepestDescent
-
- SteepestDescent - Class in etomica.math.numerical
-
- SteepestDescent(FunctionMultiDimensionalDifferentiable) - Constructor for class etomica.math.numerical.SteepestDescent
-
- steepestDescentAlgorithm() - Method in class etomica.conjugategradient.SteepestDescent
-
Steepest Descent solution for
Ax = b
- stepCount - Variable in class etomica.action.ActionIntegrate
-
- stepCount - Variable in class etomica.action.activity.ActivityIntegrate
-
- stepCount - Variable in class etomica.data.DataPumpListenerPow
-
- stepCount - Variable in class etomica.integrator.Integrator
-
- stepCount - Static variable in class etomica.util.Debug
-
Provides step count to other pieces of code that want to know the step
count.
- stepcount - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- stepFactor - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
-
- stepFinished() - Method in class etomica.integrator.IntegratorEventManager
-
- stepFrac - Variable in class etomica.overlap.IntegratorOverlap
-
- stepLength - Variable in class etomica.dimer.IntegratorDimerMin
-
- steps - Variable in class etomica.AlkaneEH.CH4NVT.Param
-
- steps - Variable in class etomica.AlkaneEH.DHS_NVT.Param
-
- steps - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- steps - Variable in class etomica.dielectric.DHS_NVT.Param
-
- steps - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- steps - Variable in class etomica.dielectric.TIP4P_NVT.Param
-
- steps - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- steps - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
-
- steps - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
-
- steps - Variable in class etomica.interfacial.LJMC.LjMC3DParams
-
- steps - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- steps - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
-
- steps - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- steps - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- steps - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
-
- steps - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- steps - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- steps - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- stepSize - Variable in class etomica.integrator.mcmove.MCMoveBoxStep
-
- stepSize - Variable in class etomica.integrator.mcmove.MCMoveStep
-
- stepSizeMax - Variable in class etomica.integrator.mcmove.MCMoveBoxStep
-
- stepSizeMax - Variable in class etomica.integrator.mcmove.MCMoveStep
-
- stepSizeMin - Variable in class etomica.integrator.mcmove.MCMoveBoxStep
-
- stepSizeMin - Variable in class etomica.integrator.mcmove.MCMoveStep
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
-
- stepsPerBlock - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
-
- stepStarted() - Method in class etomica.integrator.IntegratorEventManager
-
- stereodegrees - Static variable in class org.jmol.script.Token
-
- stillOnPolymer0 - Variable in class etomica.atom.iterator.ANIntergroupExchange
-
- stokeslet(double) - Method in class etomica.modules.droplet.IntegratorDroplet
-
- STOP - Static variable in class etomica.util.Debug
-
what step of the integrator should the simulation bail
set this to prevent Etomica from running for a long time while
outputting debugging information (potentially filling up the disk)
- stopAtom - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- stopNow - Variable in class etomica.modules.clustergenerator.MyApplet
-
- stopper - Variable in class etomica.modules.clustergenerator.MyApplet
-
- Stopper() - Constructor for class etomica.modules.clustergenerator.MyApplet.Stopper
-
- stopRotate() - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- stopRotate() - Method in class etomica.graphics.DisplayCanvas
-
- stopRotate() - Method in class etomica.graphics.DisplayPolytopeCanvasG3DSys
-
- stopRotation() - Method in class g3dsys.control.G3DSys
-
- stopSimulation - Variable in class etomica.virial.GUI.models.ModelSimulationEnvironment
-
- storeAngularMomentum - Variable in class etomica.integrator.IntegratorRigidIterative
-
- StoredIterator - Class in etomica.graph.iterators
-
- StoredIterator(byte) - Constructor for class etomica.graph.iterators.StoredIterator
-
- straightness - Static variable in class org.jmol.script.Token
-
- StrainColorScheme - Class in etomica.modules.materialfracture
-
- StrainColorScheme() - Constructor for class etomica.modules.materialfracture.StrainColorScheme
-
- strandcount - Static variable in class org.jmol.script.Token
-
- strandcountformeshribbon - Static variable in class org.jmol.script.Token
-
- strandcountforstrands - Static variable in class org.jmol.script.Token
-
- strands - Variable in class etomica.graph.property.FFTDecomposition
-
- strands - Variable in class etomica.graph.property.IsFFT
-
- strands - Static variable in class org.jmol.script.Token
-
- streamOut(OutputStream) - Method in class etomica.graph.viewer.GraphMap
-
- string - Static variable in class org.jmol.script.Token
-
- stringBuilder - Variable in class etomica.graphics.DisplayTable
-
- StringFeature - Class in etomica.compatibility
-
- StringFeature(String, String) - Constructor for class etomica.compatibility.StringFeature
-
- stringiWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- stringOmega2 - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- Strings - Class in etomica.util
-
Non-instantiable class providing a few static methods for String manipulation.
- stringToDim(String) - Static method in class etomica.units.gui.UnitFilter
-
- stringToUnit(String) - Static method in class etomica.units.gui.UnitFilter
-
- stringToUnitSystem(String) - Static method in class etomica.units.gui.UnitFilter
-
- stringWidth(String) - Method in class org.jmol.util.JmolFont
-
- stringWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- stringWV - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2DGraphic
-
- StringXBuilder - Class in org.jmol.util
-
Interesting thing here is that JavaScript is 3x faster than Java in handling strings.
- StringXBuilder() - Constructor for class org.jmol.util.StringXBuilder
-
- strparam - Static variable in class org.jmol.script.Token
-
- strproperty - Static variable in class org.jmol.script.Token
-
- strucid - Static variable in class org.jmol.script.Token
-
- strucno - Static variable in class org.jmol.script.Token
-
- struct - Variable in class etomica.data.meter.MeterStructureFactor
-
- structure(String) - Method in class etomica.server.resources.SimulationResource
-
- structure - Static variable in class org.jmol.script.Token
-
- strutdefaultradius - Static variable in class org.jmol.script.Token
-
- strutlengthmaximum - Static variable in class org.jmol.script.Token
-
- struts - Static variable in class org.jmol.script.Token
-
- strutsmultiple - Static variable in class org.jmol.script.Token
-
- strutspacing - Static variable in class org.jmol.script.Token
-
- Stuff(PotentialGroup, PotentialGroup, ISpecies) - Constructor for class etomica.parser.ParserLAMMPS.Stuff
-
- stx3leval(double, double, double) - Static method in class etomica.potential.P2O2Bartolomei
-
- sType - Variable in class etomica.virial.Species7SiteRigidSF6
-
- Sub - Class in etomica.graph.operations
-
- Sub() - Constructor for class etomica.graph.operations.Sub
-
- sub(Matrix3f) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to the matrix difference of itself and matrix
m1 (this = this - m1).
- sub(Matrix4f) - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to the matrix difference of itself and matrix
m1 (this = this - m1).
- sub(Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the vector difference of itself and tuple
t1 (this = this - t1).
- sub2(Tuple3f, Tuple3f) - Method in class org.jmol.util.Tuple3f
-
Sets the value of this tuple to the vector difference of tuple t1 and t2
(this = t1 - t2).
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- subBlockSize - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- subBox - Variable in class etomica.metastable.MeterDensityDistribution
-
- subClusterValues - Variable in class etomica.virial.ClusterSumIC
-
- subCriterion - Variable in class etomica.nbr.CriterionAdapter
-
- subCriterion - Variable in class etomica.nbr.molecule.CriterionAdapterMolecular
-
- subData - Variable in class etomica.metastable.MeterDensityDistribution
-
- subDataInfo - Variable in class etomica.data.types.DataGroup.DataInfoGroup
-
- subDataInfo - Variable in class etomica.data.types.DataGroup.DataInfoGroupFactory
-
- subIntegrator - Variable in class etomica.thermointegration.IntegratorThermodynamic
-
- subst - Variable in class etomica.graph.operations.BiComponentSubst.BiComponentSubstParameters
-
- subst - Variable in class etomica.graph.operations.ComponentSubst.ComponentSubstParameters
-
- substMinMulti(Graph) - Method in class etomica.virial.cluster.VirialDiagrams
-
- substring(int) - Method in class org.jmol.util.StringXBuilder
-
- substring2(int, int) - Method in class org.jmol.util.StringXBuilder
-
- substructure - Static variable in class org.jmol.script.Token
-
- substSet - Variable in class etomica.virial.PYGenerator.IteratorEF
-
- subtract(BigIntegerPoly) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Subtract another polynomial
- subtract(BigSurdVec) - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Subtract another number.
- subtract(BigSurd) - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Subtract another number.
- subtract(Rational) - Method in class etomica.veos.bigdecimal.Rational
-
Subtract another fraction.
- subtract(BigInteger) - Method in class etomica.veos.bigdecimal.Rational
-
Subtract an integer.
- subtract(int) - Method in class etomica.veos.bigdecimal.Rational
-
Subtract an integer.
- subtractApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- subtractApprox - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- subtractHalf - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- subtractHalf - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- subtractHalf - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- subtractRound(BigDecimal, BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Subtract and round according to the larger of the two ulp's.
- subtractRound(BigComplex, BigComplex) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Subtract and round according to the larger of the two ulp's.
- subtractWhat - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- subtractWhat - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- Sulfur - Class in etomica.chem.elements
-
Class for the Sulfur element.
- Sulfur(String) - Constructor for class etomica.chem.elements.Sulfur
-
- Sulfur(String, double) - Constructor for class etomica.chem.elements.Sulfur
-
- sulfurType - Variable in class etomica.modules.sam.IntegratorVelocityVerletSAM
-
- sum - Variable in class etomica.data.AccumulatorAverageBlockless.AllData
-
- sum - Variable in class etomica.data.AccumulatorAverageBlockless
-
- sum - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
-
- sum - Variable in class etomica.data.AccumulatorAverageFixed
-
- sum - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- sum - Variable in class etomica.data.histogram.HistogramSimple
-
- sum - Variable in class etomica.freeenergy.npath.PotentialCalculationDUDW
-
- Sum - Class in etomica.graph.operations
-
- Sum() - Constructor for class etomica.graph.operations.Sum
-
- sum - Variable in class etomica.interfacial.MeterWallForce.PotentialCalculationWallForce
-
- sum - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- sum - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- sum - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- sum - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- sum - Variable in class etomica.meam.PotentialCalculationEnergySumEAM
-
- sum - Variable in class etomica.modules.insertion.InsertionGraphic.MeterWidom
-
- sum - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- sum() - Method in class etomica.potential.EwaldSumMolecules
-
- sum - Variable in class etomica.potential.PotentialCalculationEnergySum
-
- sum - Variable in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
- sum(ClusterDiagram[], ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Generates the set of diagrams obtained by adding the second set to the first set.
- sum - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- sum - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- sum - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- sum - Static variable in class org.jmol.script.Token
-
- sum1 - Variable in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- sum1 - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
-
- sum1 - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- sum2 - Variable in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- sum2 - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- sum2 - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- sum2 - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- sum2 - Static variable in class org.jmol.script.Token
-
- sum_separate - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- sumBlockSquare - Variable in class etomica.data.AccumulatorAverageFixed
-
- sumBlockSquare - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- sumCheck - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- sumDelete - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- sumInsert - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- summary(Parser.CommandVariable) - Method in class etomica.graph.engine.Interpreter
-
- summer - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- summer - Variable in class etomica.normalmode.NormalModesMolecular
-
- sums - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- sums - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- sums - Variable in class etomica.data.histogram.HistogramNotSoSimple
-
- sums - Variable in class etomica.data.histogram.HistogramReweightedData
-
- sums - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
- sums - Variable in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
- sums - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoffLS
-
- sumSqD2 - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- sumSqD2D - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- sumSqD3 - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- sumSqD3D - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- sumSqDy - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- sumSquare - Variable in class etomica.data.AccumulatorAverageBlockless.AllData
-
- sumSquare - Variable in class etomica.data.AccumulatorAverageBlockless
-
- sumSquare - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
-
- sumSquare - Variable in class etomica.data.AccumulatorAverageFixed
-
- sumSquare - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- sumWeights - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSinkReweightedDeltaU
-
- SuperImposeGraphs(Graph, Graph) - Static method in class etomica.virial.IEGenerator
-
- support - Variable in class etomica.graphics.Display
-
- suppressAction - Variable in class etomica.graphics.DeviceSlider
-
- suppressBoxLengthWarning - Variable in class etomica.nbr.cell.NeighborCellManager
-
- suppressMakeAgent - Variable in class etomica.potential.P2SquareWellRobust
-
- surface - Static variable in class org.jmol.script.Token
-
- surfaceColor - Variable in class etomica.modules.droplet.ColorSchemeDropletSurface
-
- surfaceCursor - Variable in class etomica.modules.sam.CriterionTether3
-
- surfaceDim - Variable in class etomica.data.DataProcessorInterfacialTension
-
- surfacedistance - Static variable in class org.jmol.script.Token
-
- surfacePosition - Variable in class etomica.modules.sam.SamGraphic.ModifierWallPosition
-
- surfaceSet - Variable in class org.jmol.util.MeshSurface
-
- SurfaceTensionMapped - Class in etomica.surfacetension
-
DataProcessor that adds in mapped average contributions to the surface
tension.
- SurfaceTensionMapped(Space, Box, ISpecies, PotentialMaster) - Constructor for class etomica.surfacetension.SurfaceTensionMapped
-
- surfaceType - Variable in class etomica.modules.sam.CriterionTether3
-
- surfactant - Variable in class etomica.modules.interfacial.InterfacialSW
-
- surfactantProfileMeter - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- surfactantProfilePump - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- sv - Variable in class etomica.potential.P2SpheroPolyhedron
-
- sValue(Token) - Static method in class org.jmol.script.ScriptVariable
-
- SVG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverter
-
SVG file extension
- SVG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverter.SVGFileFilter
-
- SVG_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverterURLSource
-
SVG file extension
- SVGConverter - Class in etomica.graph.view.rasterizer
-
This application can be used to convert SVG images to raster images.
- SVGConverter() - Constructor for class etomica.graph.view.rasterizer.SVGConverter
-
- SVGConverter(SVGConverterController) - Constructor for class etomica.graph.view.rasterizer.SVGConverter
-
- SVGConverter.SVGFileFilter - Class in etomica.graph.view.rasterizer
-
Convenience class to filter svg files
- SVGConverterController - Interface in etomica.graph.view.rasterizer
-
Interface for controlling some aspectes of the
SVGConverter operation.
- SVGConverterDocumentSource - Class in etomica.graph.view.rasterizer
-
- SVGConverterDocumentSource(SVGDocument) - Constructor for class etomica.graph.view.rasterizer.SVGConverterDocumentSource
-
- SVGConverterException - Exception in etomica.graph.view.rasterizer
-
Describes an error condition in SVGConverter
- SVGConverterException(String) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
-
- SVGConverterException(String, Object[]) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
-
- SVGConverterException(String, Object[], boolean) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
-
- SVGConverterException(String, boolean) - Constructor for exception etomica.graph.view.rasterizer.SVGConverterException
-
- SVGConverterFileSource - Class in etomica.graph.view.rasterizer
-
Describes a file source for the SVGConverter
- SVGConverterFileSource(File) - Constructor for class etomica.graph.view.rasterizer.SVGConverterFileSource
-
- SVGConverterFileSource(File, String) - Constructor for class etomica.graph.view.rasterizer.SVGConverterFileSource
-
- SVGConverterSource - Interface in etomica.graph.view.rasterizer
-
Interface used to handle both Files and URLs in the
SVGConverter
- SVGConverterURLSource - Class in etomica.graph.view.rasterizer
-
- SVGConverterURLSource(String) - Constructor for class etomica.graph.view.rasterizer.SVGConverterURLSource
-
- SVGFileFilter() - Constructor for class etomica.graph.view.rasterizer.SVGConverter.SVGFileFilter
-
- SVGZ_EXTENSION - Static variable in class etomica.graph.view.rasterizer.SVGConverterURLSource
-
- swap - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- swap(int, int) - Method in class etomica.virial.cluster.ClusterDiagram
-
Swaps point1 and point2.
- swap(Object[], int, int) - Static method in class org.jmol.util.ArrayUtil
-
- swap0n(byte) - Method in class etomica.virial.cluster.VirialDiagrams
-
- swap0n(byte, int, int, boolean) - Method in class etomica.virial.cluster.VirialDiagramsMix2
-
- swap0n(byte) - Method in class etomica.virial.cluster.VirialDiagramsPT
-
- swapAllAndCompare(boolean, ClusterDiagram, int[]) - Static method in class etomica.virial.cluster.ClusterGenerator
-
- SwapFactory() - Constructor for class etomica.integrator.mcmove.MCMoveSwapConfiguration.SwapFactory
-
- SwapFactory() - Constructor for class etomica.virial.paralleltempering.MCMoveSwapCluster.SwapFactory
-
- swapInt(int[], int, int) - Static method in class org.jmol.util.ArrayUtil
-
- swappedBoxes() - Method in interface etomica.integrator.IntegratorPT.MCMoveSwap
-
- swappedBoxes() - Method in class etomica.integrator.mcmove.MCMoveSwapConfiguration
-
Implementation of MCMoveSwap interface
- swappedBoxes() - Method in class etomica.virial.paralleltempering.MCMoveSwapCluster
-
Implementation of MCMoveSwap interface
- sweepRadius - Variable in class etomica.atom.AtomTypeSpheroPolyhedron
-
- switchFac - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- switchFac - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- Swmd - Class in etomica.modules.swmd
-
- Swmd(Space) - Constructor for class etomica.modules.swmd.Swmd
-
- SWMD2D - Class in etomica.simulation.prototypes
-
Simple square-well molecular dynamics simulation in 2D
- SWMD2D() - Constructor for class etomica.simulation.prototypes.SWMD2D
-
- SWMD3D - Class in etomica.simulation.prototypes
-
Simple square-well molecular dynamics simulation in 3D
- SWMD3D() - Constructor for class etomica.simulation.prototypes.SWMD3D
-
- SwmdGraphic - Class in etomica.modules.swmd
-
- SwmdGraphic(Swmd, Space) - Constructor for class etomica.modules.swmd.SwmdGraphic
-
- SwmdGraphic.Applet - Class in etomica.modules.swmd
-
- SwmdGraphic.DataSinkExcludeOverlap - Class in etomica.modules.swmd
-
- SwmdGraphic.ModifierAtomDiameter - Class in etomica.modules.swmd
-
- sx1 - Variable in class etomica.dimer.P1LepsHarmonic
-
- sx2 - Variable in class etomica.dimer.P1LepsHarmonic
-
- sy1 - Variable in class etomica.dimer.P1LepsHarmonic
-
- sy2 - Variable in class etomica.dimer.P1LepsHarmonic
-
- symbol - Variable in class etomica.chem.elements.Element
-
- symbol() - Method in class etomica.units.CompoundUnit
-
- symbol() - Method in enum etomica.units.Prefix
-
Symbol used to show that prefix is part of the unit.
- symbol() - Method in class etomica.units.PrefixedUnit
-
- symbol() - Method in class etomica.units.SimpleUnit
-
- symbol() - Method in class etomica.units.systems.LJ.LJUnit
-
- symbol() - Method in interface etomica.units.Unit
-
Returns the symbol of unit, such as "g" for grams.
- symbol - Static variable in class org.jmol.script.Token
-
- symmetry - Static variable in class org.jmol.script.Token
-
- symop - Static variable in class org.jmol.script.Token
-
- syncmouse - Static variable in class org.jmol.script.Token
-
- syncscript - Static variable in class org.jmol.script.Token
-
- SZ_INT - Static variable in class etomica.graph.traversal.BitmapUtils
-
- SZ_LONG - Static variable in interface etomica.graph.model.Bitmap
-
T
- t - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ColorSchemeDeviation
-
- T - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- T - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
-
- T - Variable in class etomica.freeenergy.npath.SimLattice.LjMC3DParams
-
- T - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
-
- T - Variable in class etomica.interfacial.LJMC.LjMC3DParams
-
- T - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- T - Variable in class etomica.liquidLJ.LjMC3D.LjMC3DParams
-
- t - Variable in class etomica.math.numerical.AkimaSpline
-
- t - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- T - Variable in class etomica.normalmode.HarmonicCrystalSsFccNxy.Params
-
- T - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
-
- t - Variable in class etomica.virial.ClusterPY
-
- t1 - Variable in class etomica.meam.ParameterSetMEAM
-
- T1ij - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- T1ij - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- T1ik - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- T1RHOj0 - Static variable in class etomica.meam.PotentialMEAM
-
- t2 - Variable in class etomica.meam.ParameterSetMEAM
-
- T2ij - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- T2RHOj0 - Static variable in class etomica.meam.PotentialMEAM
-
- t3 - Variable in class etomica.meam.ParameterSetMEAM
-
- T3ij - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- T3RHOj0 - Static variable in class etomica.meam.PotentialMEAM
-
- ta - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- taa - Static variable in class etomica.potential.P2O2Bartolomei
-
- taaMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- taaPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- TABBED_PANE - Static variable in class etomica.graphics.SimulationGraphic
-
- tabbedPane - Variable in class etomica.graphics.SimulationPanel
-
- tableModel() - Method in class etomica.graphics.DisplayTable
-
- tableRowCountChanged(DataSinkTable) - Method in interface etomica.data.DataTableListener
-
Method called to indicate that the number of rows in the
table has changed.
- tableRowCountChanged(DataSinkTable) - Method in class etomica.graphics.DisplayTable
-
Part of the DataTableListener interface.
- tableRowHeadersChanged(DataSinkTable) - Method in interface etomica.data.DataTableListener
-
Method called to indicate that the row headers in the table have
changed.
- tableRowHeadersChanged(DataSinkTable) - Method in class etomica.graphics.DisplayTable
-
- tag - Variable in class etomica.data.DataDistributer
-
- tag - Variable in class etomica.data.DataDump
-
- tag - Variable in class etomica.data.DataFork
-
- tag - Variable in class etomica.data.DataGroupSplitter
-
- tag - Variable in class etomica.data.DataProcessor
-
- tag - Variable in class etomica.data.DataSourceFunction
-
- tag - Variable in class etomica.data.DataSourceGroup
-
- tag - Variable in class etomica.data.DataSourceIndependentSimple
-
- tag - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
-
- tag - Variable in class etomica.data.DataSourceRmsVelocity
-
- tag - Variable in class etomica.data.DataSourceScalar
-
- tag - Variable in class etomica.data.DataSourceTensorVirialHard
-
- tag - Variable in class etomica.data.DataSourceUniform
-
- tag - Variable in class etomica.data.DataSplitter
-
- tag - Variable in class etomica.data.HistogramDataSource
-
- tag - Variable in class etomica.data.meter.MeterDihedralAngle
-
- tag - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- tag - Variable in class etomica.data.meter.MeterHyperVirial
-
- tag - Variable in class etomica.data.meter.MeterMomentumCOM
-
- tag - Variable in class etomica.data.meter.MeterPositionCOM
-
- tag - Variable in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
-
- tag - Variable in class etomica.data.meter.MeterPressureHardTensor
-
- tag - Variable in class etomica.data.meter.MeterPressureTensor
-
- tag - Variable in class etomica.data.meter.MeterPressureTensorFromIntegrator
-
- tag - Variable in class etomica.data.meter.MeterProfile
-
- tag - Variable in class etomica.data.meter.MeterProfileByAtoms
-
- tag - Variable in class etomica.data.meter.MeterProfileByVolume
-
- tag - Variable in class etomica.data.meter.MeterRDF
-
- tag - Variable in class etomica.data.meter.MeterRDFPC
-
- tag - Variable in class etomica.data.meter.MeterStructureFactor
-
- tag - Variable in class etomica.data.meter.MeterTensorVelocity
-
- tag - Variable in class etomica.freeenergy.npath.DataSourceEnergies
-
- tag - Variable in class etomica.gaussianwork.MeterBoltzmannA
-
- tag - Variable in class etomica.gaussianwork.MeterBoltzmannB
-
- tag - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- tag - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- tag - Variable in class etomica.liquidLJ.MeterPotentialEnergyCutoff
-
- tag - Variable in class etomica.liquidLJ.MeterPU
-
- tag - Variable in class etomica.liquidLJ.MeterPUCut
-
- tag - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- tag - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- tag - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- tag - Variable in class etomica.mappedvirial.MeterMeanForce
-
- tag - Variable in class etomica.models.nitrogen.MeterBoltzmann
-
- tag - Variable in class etomica.models.nitrogen.MeterBoltzmannRotPerturb
-
- tag - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- tag - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- tag - Variable in class etomica.models.oneDHardRods.MeterNMCBaskets
-
- tag - Variable in class etomica.models.oneDHardRods.MeterNormalModeCoordinate
-
- tag - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
-
- tag - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- tag - Variable in class etomica.modules.chainequilibrium.MeterChainLength
-
- tag - Variable in class etomica.modules.droplet.MeterDeformation
-
- tag - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- tag - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile.DataSourceVirialProfile
-
- tag - Variable in class etomica.modules.interfacial.MeterOrientation
-
- tag - Variable in class etomica.modules.mu.DataSourceWallPressureMu
-
- tag - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- tag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- tag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- tag - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- tag - Variable in class etomica.modules.rosmosis.MeterFlux
-
- tag - Variable in class etomica.modules.rosmosis.MeterOsmoticPressure
-
- tag - Variable in class etomica.modules.sam.MeterTilt
-
- tag - Variable in class etomica.modules.statistics.DataCollector
-
- tag - Variable in class etomica.normalmode.DataSourceFE
-
- tag - Variable in class etomica.normalmode.DataSourceFEHistogram
-
- tag - Variable in class etomica.normalmode.DataSourceImposedFEFit
-
- tag - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
-
- tag - Variable in class etomica.normalmode.DataSourcePMu
-
- tag - Variable in class etomica.normalmode.DataSourcePN
-
- tag - Variable in class etomica.normalmode.MeterBoltzmann
-
- tag - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
-
- tag - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- tag - Variable in class etomica.normalmode.MeterBoltzmannTarget
-
- tag - Variable in class etomica.normalmode.MeterDADB
-
- tag - Variable in class etomica.normalmode.MeterDDP
-
- tag - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- tag - Variable in class etomica.normalmode.MeterDirectSamplingTarget
-
- tag - Variable in class etomica.normalmode.MeterDP
-
- tag - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- tag - Variable in class etomica.normalmode.MeterPlaneSlip
-
- tag - Variable in class etomica.normalmode.MeterSamplingHarmonic
-
- tag - Variable in class etomica.normalmode.MeterSamplingTarget
-
- tag - Variable in class etomica.normalmode.MeterSolidDA
-
- tag - Variable in class etomica.normalmode.MeterSolidDACut
-
- tag - Variable in class etomica.normalmode.MeterSolidMirror
-
- tag - Variable in class etomica.normalmode.MeterSolidProps
-
- tag - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- tag - Variable in class etomica.normalmode.MeterTargetTP
-
- tag - Variable in class etomica.normalmode.MeterTilt
-
- tag - Variable in class etomica.normalmode.MeterTiltHistogram
-
- tag - Variable in class etomica.normalmode.MeterTiltRotation
-
- tag - Variable in class etomica.normalmode.MeterTiltRotationStdev
-
- tag - Variable in class etomica.normalmode.MeterWorkBennetHarmonic
-
- tag - Variable in class etomica.normalmode.MeterWorkBennetTarget
-
- tag - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
-
- tag - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- tag - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- tag - Variable in class etomica.normalmode.MeterWorkHarmonicUmbrella
-
- tag - Variable in class etomica.normalmode.MeterWorkTargetBennet
-
- tag - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- tag - Variable in class etomica.normalmode.MeterWorkTargetPhaseSpace
-
- tag - Variable in class etomica.normalmode.MeterWorkTargetUmbrella
-
- tag - Variable in class etomica.normalmode.MeterWorkUmbrellaHarmonic
-
- tag - Variable in class etomica.normalmode.MeterWorkUmbrellaTarget
-
- tag - Variable in class etomica.overlap.MeterOverlap
-
- tagged - Variable in class etomica.modules.chainequilibrium.MeterChainLength.AtomTag
-
- tagManager - Variable in class etomica.modules.chainequilibrium.MeterChainLength
-
- tags - Variable in class etomica.data.DataInfoFactory
-
- tags - Variable in class etomica.graphics.DataTagBag
-
- tags - Variable in class etomica.modules.statistics.DataProcessorBounds
-
- tailType - Variable in class etomica.modules.interfacial.InterfacialSW
-
- tajmols - Static variable in class etomica.potential.P2O2Bartolomei
-
- tajmolsMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- tajmolsPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- tajp1 - Static variable in class etomica.potential.P2O2Bartolomei
-
- tajp1MRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- tajp1PT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- tajpn - Static variable in class etomica.potential.P2O2Bartolomei
-
- tajpnMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- tajpnPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- takeStep(Vector[], Vector[], double) - Method in class etomica.action.ActionMinimizeEnergy
-
- tan() - Method in class etomica.math.Complex
-
Tangent of this Complex number (doesn't change this Complex number).
- tan(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The trigonometric tangent.
- tangledMolecules - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- tangledMolecules - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- tangledMolecules - Variable in class etomica.virial.MCMoveClusterRingScale
-
- tanh(BigDecimal) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
The hyperbolic tangent.
- taperOrder - Variable in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- taperOrder - Variable in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- target - Variable in class etomica.atom.iterator.ApiIndexList
-
- TARGET - Static variable in class etomica.overlap.DataOverlap
-
- targetAcc - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
-
- targetAccumulator - Variable in class etomica.virial.overlap.DataSourceVirialOverlap
-
- targetAccumulator - Variable in class etomica.virial.overlap.DataVirialOverlap
-
- targetAction - Variable in class etomica.graphics.DeviceButton
-
- targetAction - Variable in class etomica.graphics.DeviceButtonGroup
-
- targetAction - Variable in class etomica.graphics.DeviceSlider
-
- targetAction - Variable in class etomica.graphics.DeviceSpinner
-
- targetAction - Variable in class etomica.zeolite.DeviceButtonSingle
-
- targetAtom - Variable in class etomica.atom.iterator.ApiIntergroup
-
- targetAtom - Variable in class etomica.atom.iterator.TripletInnerSequential
-
- targetAtom - Variable in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- targetAvg - Variable in class etomica.overlap.DataOverlap
-
- targetAvg - Variable in class etomica.virial.overlap.DataVirialOverlap.FullResult
-
- targetCluster - Variable in class etomica.virial.MeterVirialBDBin
-
- targetCluster - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- targetCluster - Variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- targetCluster - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- targetCluster - Variable in class etomica.virial.MeterVirialIC
-
- targetCluster - Variable in class etomica.virial.simulations.ModifierTPI
-
- targetDataInterval - Variable in class etomica.normalmode.SimOverlapModule
-
- targetErr - Variable in class etomica.virial.overlap.DataVirialOverlap.FullResult
-
- targetIndex - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- targetMolecule - Variable in class etomica.modules.sam.CriterionTether3
-
- targetSum - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- targetTemp - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- targetTemp - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- targHist - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- targPiHist - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- targShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- targShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- targShape - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- tau - Variable in class etomica.models.co2.PNGCPM.GCPMAgent
-
- tau - Variable in class etomica.models.water.P2Water4PSoft
-
- tauAll - Variable in class etomica.models.co2.PNCO2GCPM
-
- tauC - Variable in class etomica.models.co2.PNCO2GCPM
-
- tauO - Variable in class etomica.models.co2.PNCO2GCPM
-
- tav1() - Method in class etomica.meam.PotentialMEAM
-
- tav2() - Method in class etomica.meam.PotentialMEAM
-
- tav3() - Method in class etomica.meam.PotentialMEAM
-
- tb - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- tbet - Static variable in class etomica.potential.P2O2Bartolomei
-
- tbetMRCI - Static variable in class etomica.potential.P2O2Bartolomei
-
- tbetPT2 - Static variable in class etomica.potential.P2O2Bartolomei
-
- Tc - Static variable in class etomica.modules.adsorption.EOSSW
-
- tCompute(double[][], double[][], int, int, double) - Static method in class etomica.virial.OrnsteinZernike
-
- TE(IData) - Method in interface etomica.data.IData
-
Times-equals (*=) operation.
- TE(double) - Method in interface etomica.data.IData
-
Times-equals (*=) operation, multiplying all values in data by given
value.
- TE(IData) - Method in class etomica.data.types.DataDouble
-
Times-equals (*=) operation.
- TE(double) - Method in class etomica.data.types.DataDouble
-
Times-equals (*=) operation.
- TE(IData) - Method in class etomica.data.types.DataDoubleArray
-
Times-equals (*=) operation.
- TE(double) - Method in class etomica.data.types.DataDoubleArray
-
Times-equals (*=) operation.
- TE(IData) - Method in class etomica.data.types.DataDoubleBDArray
-
Times-equals (*=) operation.
- TE(double) - Method in class etomica.data.types.DataDoubleBDArray
-
Times-equals (*=) operation.
- TE(IData) - Method in class etomica.data.types.DataGroup
-
- TE(double) - Method in class etomica.data.types.DataGroup
-
- TE(IData) - Method in class etomica.data.types.DataTensor
-
Times-equals (*=) operation.
- TE(double) - Method in class etomica.data.types.DataTensor
-
Times-equals (*=) operation.
- TE(IData) - Method in class etomica.data.types.DataVector
-
Times-equals (*=) operation.
- TE(double) - Method in class etomica.data.types.DataVector
-
Times-equals (*=) operation.
- TE(double) - Method in class etomica.math.Quaternion
-
Multiplies all the components of the Quaternion q by the given scalar
- TE(double) - Method in interface etomica.space.Tensor
-
"Times equals" (*=) operation, replaces each element of this tensor by its current value times the given scalar
- TE(Tensor) - Method in interface etomica.space.Tensor
-
"Times equals" (*=) operation, as matrix multiplication.
- TE(Vector) - Method in interface etomica.space.Vector
-
Times-equals (*=) operation.
- TE(double) - Method in interface etomica.space.Vector
-
Multiplies all components by a constant.
- TE(double) - Method in class etomica.space1d.Tensor1D
-
- TE(Tensor) - Method in class etomica.space1d.Tensor1D
-
- TE(double) - Method in class etomica.space1d.Vector1D
-
- TE(Vector) - Method in class etomica.space1d.Vector1D
-
- TE(double) - Method in class etomica.space2d.Tensor2D
-
- TE(Tensor) - Method in class etomica.space2d.Tensor2D
-
- TE(double) - Method in class etomica.space2d.Vector2D
-
- TE(Vector) - Method in class etomica.space2d.Vector2D
-
- TE(double) - Method in class etomica.space3d.Tensor3D
-
- TE(Tensor) - Method in class etomica.space3d.Tensor3D
-
- TE(double) - Method in class etomica.space3d.Vector3D
-
- TE(Vector) - Method in class etomica.space3d.Vector3D
-
- TE(double) - Method in class etomica.spaceNd.TensorND
-
- TE(Tensor) - Method in class etomica.spaceNd.TensorND
-
- TE(double) - Method in class etomica.spaceNd.VectorND
-
- TE(Vector) - Method in class etomica.spaceNd.VectorND
-
- TE(IBigValue) - Method in class etomica.veos.BigValue
-
Times-equals (*=) operation.
- TE(double) - Method in class etomica.veos.BigValue
-
Times-equals (*=).
- TE(IBigValue) - Method in interface etomica.veos.IBigValue
-
Times-equals (*=) operation.
- TE(double) - Method in interface etomica.veos.IBigValue
-
Times-equals (*=).
- TE(IBigValue) - Method in class etomica.veos.MyBigDecimal
-
Times-equals (*=) operation.
- TE(double) - Method in class etomica.veos.MyBigDecimal
-
Times-equals (*=).
- TEAL - Static variable in class org.jmol.util.Colix
-
- TEln(double) - Method in class etomica.veos.BigValue
-
Times-equals (*=) operation, multiplying by a value given as its logarithm.
- temp - Variable in class etomica.integrator.IntegratorVelocityVerletShake
-
- temp - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- temp - Variable in class etomica.models.nitrogen.BoundaryDeformablePeriodicSwitch
-
- temp - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- temp - Variable in class etomica.space3d.Orientation3D
-
- temp2 - Variable in class etomica.space3d.Orientation3D
-
- tempAngularVelocity - Variable in class etomica.integrator.IntegratorRigidIterative
-
- tempAngularVelocity - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- tempAxesTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- temperature - Variable in class etomica.action.BoxQuench
-
- temperature - Variable in class etomica.action.BoxRandomizeMomenta
-
- temperature - Variable in class etomica.action.BoxScaleMomenta
-
- temperature - Variable in class etomica.AlkaneEH.DHS_NVT.Param
-
- temperature - Variable in class etomica.AlkaneEH.DLJ_NVT_1site.Param
-
- temperature - Variable in class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT.AceticAcidMCParam
-
- temperature - Variable in class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
-
- temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
-
- temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.data.meter.MeterHyperVirial
-
- temperature - Variable in class etomica.data.meter.MeterPressure
-
- temperature - Variable in class etomica.data.meter.MeterWidomInsertion
-
- temperature - Variable in class etomica.dielectric.DHS_NVT.Param
-
- temperature - Variable in class etomica.dielectric.DLJ_NVT_1site.Param
-
- temperature - Variable in class etomica.gaussianwork.MeterBoltzmannA
-
- temperature - Variable in class etomica.gaussianwork.MeterBoltzmannB
-
- temperature - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- temperature - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- temperature - Variable in class etomica.integrator.IntegratorBox
-
- temperature - Variable in class etomica.integrator.IntegratorManagerMC
-
- temperature - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- temperature - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- temperature - Variable in class etomica.liquidLJ.MeterPU
-
- temperature - Variable in class etomica.liquidLJ.MeterPUCut
-
- temperature - Variable in class etomica.liquidLJ.MeterPUCutLS
-
- temperature - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- temperature - Variable in class etomica.liquidLJ.MeterWidomInsertionP
-
- temperature - Variable in class etomica.mappedRdf.MappedRdf.LJMDParams
-
- temperature - Variable in class etomica.mappedvirial.MappedU.LJMDParams
-
- temperature - Variable in class etomica.mappedvirial.MappedVirialLJ.LJMDParams
-
- temperature - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
-
- temperature - Variable in class etomica.meam.EFSTungsten.Params
-
- temperature - Variable in class etomica.metastable.LJmuVT.LJMCParams
-
- temperature - Variable in class etomica.metastable.LJNPT.LJMCParams
-
- temperature - Variable in class etomica.metastable.LJNVT.LJMCParams
-
- temperature - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- temperature - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- temperature - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- temperature - Variable in class etomica.models.nitrogen.MeterTargetRPMolecule
-
- temperature - Variable in class etomica.models.nitrogen.MeterTargetTPMolecule
-
- temperature - Variable in class etomica.models.nitrogen.SimDirectBetaN2RP.SimOverlapParam
-
- temperature - Variable in class etomica.models.nitrogen.SimOverlapAlphaN2TP.SimOverlapParam
-
- temperature - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RP.SimOverlapParam
-
- temperature - Variable in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling.SimOverlapParam
-
- temperature - Variable in class etomica.models.nitrogen.SimOverlapBetaN2TP.SimOverlapParam
-
- temperature - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling.SimOverlapParam
-
- temperature - Variable in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP.SimOverlapParam
-
- temperature - Variable in class etomica.models.nitrogen.SimOverlapNitrogenModel.SimOverlapParam
-
- temperature - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- temperature - Variable in class etomica.models.oneDHardRods.MeterCompareMultipleWVBrute
-
- temperature - Variable in class etomica.models.oneDHardRods.MeterCompareWVShortcut
-
- temperature - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- temperature - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd1D
-
- temperature - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- temperature - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract1D
-
- temperature - Variable in class etomica.models.oneDHardRods.MeterWidomMode
-
- temperature - Variable in class etomica.models.oneDHardRods.MeterWidomModeImaginary
-
- temperature - Variable in class etomica.models.oneDHardRods.MeterWidomModeReal
-
- temperature - Variable in class etomica.models.oneDHardRods.SimDegFreeBinning.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimDegreeFreedom3D.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImage.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImage1D.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImage1DHR.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFcc.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccBigCell.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimDifferentImageSsFccDoubleSize.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimExtensiveTest.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWaveVectors.SimOverlapMultipleWaveVectorsParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimOverlapMultipleWV3DLJ.SimOverlapMultipleWaveVectorsParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimOverlapSsNxy.SimOverlapParam
-
- temperature - Variable in class etomica.models.oneDHardRods.SimWidomMode.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd.SimParam
-
- temperature - Variable in class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract.SimParam
-
- temperature - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- temperature - Variable in class etomica.modules.adsorption.EOSSW
-
- temperature - Variable in class etomica.modules.multiharmonic.mbar.MeterMBAR
-
- temperature - Variable in class etomica.modules.multiharmonic.umbrella.MeterUmbrella
-
- temperature - Variable in class etomica.modules.render.RenderMD.RenderMDParam
-
- temperature - Variable in class etomica.modules.vle.VLESim
-
- temperature - Variable in class etomica.normalmode.DataProcessorBoltzmannFactor
-
- temperature - Variable in class etomica.normalmode.IntegratorHarmonic
-
- temperature - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- temperature - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- temperature - Variable in class etomica.normalmode.MCMoveEinsteinCrystal
-
- temperature - Variable in class etomica.normalmode.MCMoveHarmonic
-
- temperature - Variable in class etomica.normalmode.MCMoveSingleMode
-
- temperature - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- temperature - Variable in class etomica.normalmode.MCMoveVolumeSolid
-
- temperature - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- temperature - Variable in class etomica.normalmode.MeterBoltzmannHarmonic
-
- temperature - Variable in class etomica.normalmode.MeterBoltzmannHTTP
-
- temperature - Variable in class etomica.normalmode.MeterBoltzmannTarget
-
- temperature - Variable in class etomica.normalmode.MeterDADB
-
- temperature - Variable in class etomica.normalmode.MeterDDP
-
- temperature - Variable in class etomica.normalmode.MeterDirectSamplingHarmonic
-
- temperature - Variable in class etomica.normalmode.MeterDP
-
- temperature - Variable in class etomica.normalmode.MeterOverlapSwitch
-
- temperature - Variable in class etomica.normalmode.MeterSolidDA
-
- temperature - Variable in class etomica.normalmode.MeterSolidDACut
-
- temperature - Variable in class etomica.normalmode.MeterSolidMirror
-
- temperature - Variable in class etomica.normalmode.MeterSolidProps
-
- temperature - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- temperature - Variable in class etomica.normalmode.MeterTargetTP
-
- temperature - Variable in class etomica.normalmode.MeterWorkHarmonicBennet
-
- temperature - Variable in class etomica.normalmode.MeterWorkHarmonicPhaseSpace
-
- temperature - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- temperature - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- temperature - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- temperature - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- temperature - Variable in class etomica.normalmode.NormalModes1DHR
-
- temperature - Variable in class etomica.normalmode.NormalModes2D
-
- temperature - Variable in class etomica.normalmode.NormalModes3D
-
- temperature - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- temperature - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- temperature - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- temperature - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- temperature - Variable in class etomica.normalmode.SimBennet.SimBennetParam
-
- temperature - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimHarmonicUmbrella.SimBennetParam
-
- temperature - Variable in class etomica.normalmode.SimLJHTTISuper.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimLJHTTISuperHCP.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimLJVacancy.LJParams
-
- temperature - Variable in class etomica.normalmode.SimOverlap.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapLJ.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapLJModule.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSoftSphere.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereDP.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereEin.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereEinHarm.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereHCP.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereReweighting.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereSoftness.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereSuperBox.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereTP.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereTPHCP.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSoftSphereTPSlantedBox.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimOverlapSSnxy.SimOverlapParam
-
- temperature - Variable in class etomica.normalmode.SimTargetUmbrella.SimBennetParam
-
- temperature - Variable in class etomica.normalmode.SimUmbrella.SimBennetParam
-
- temperature - Variable in class etomica.normalmode.SimUmbrellaSoftSphere.SimBennetParam
-
- temperature - Variable in class etomica.normalmode.WriteS
-
- temperature - Variable in class etomica.overlap.MeterOverlap
-
- temperature - Variable in class etomica.potential.EwaldSumMolecules
-
- temperature - Variable in class etomica.potential.P2DiscreteFeynmanHibbs
-
- temperature - Variable in class etomica.potential.P2EffectiveFeynmanHibbs
-
- temperature - Variable in class etomica.potential.P2HePCKLJS.P2HeQFH
-
- temperature - Variable in class etomica.potential.P2HePCKLJS.P2HeTI
-
- temperature - Variable in class etomica.potential.P2HeSimplified.P2HeQFH
-
- temperature - Variable in class etomica.potential.P2HeSimplified.P2HeTI
-
- temperature - Variable in class etomica.potential.P2LJDipole
-
- temperature - Variable in class etomica.potential.P2LJQ
-
- temperature - Variable in class etomica.potential.P2LJQQ
-
- temperature - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- temperature - Variable in class etomica.potential.P2O2Bartolomei.P2O2TI
-
- temperature - Variable in class etomica.potential.P2SemiclassicalAtomic
-
- temperature - Variable in class etomica.potential.P2SemiclassicalMolecular
-
- temperature - Variable in class etomica.potential.PotentialCalculationPressureTensor
-
- temperature - Variable in class etomica.surfacetension.LJMC.LJMCParams
-
- Temperature - Class in etomica.units.dimensions
-
The temperature dimension.
- temperature() - Method in class etomica.units.systems.CGS
-
- temperature() - Method in class etomica.units.systems.LJ
-
- temperature() - Method in class etomica.units.systems.MKS
-
- temperature() - Method in class etomica.units.systems.UnitSystem.Sim
-
- temperature() - Method in class etomica.units.systems.UnitSystem
-
- temperature - Variable in class etomica.virial.GUI.models.ModelTemperatureAndSteps
-
- temperature - Variable in class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam
-
- temperature - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.LJTSRefLJ.VirialLJParam
-
- temperature - Variable in class etomica.virial.simulations.SimulationVirial
-
- temperature - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
-
- temperature - Variable in class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
-
- temperature - Variable in class etomica.virial.simulations.VirialAceticAcid.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
-
- temperature - Variable in class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
-
- temperature - Variable in class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
-
- temperature - Variable in class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2.VirialCO2Param
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
-
- temperature - Variable in class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
-
- temperature - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
-
- temperature - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
-
- temperature - Variable in class etomica.virial.simulations.VirialExternalFieldOverlapRho.VirialExternalFieldParam
-
- temperature - Variable in class etomica.virial.simulations.VirialGCPM.VirialGCPMParam
-
- temperature - Variable in class etomica.virial.simulations.VirialH2OGCPMD.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- temperature - Variable in class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
-
- temperature - Variable in class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
-
- temperature - Variable in class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- temperature - Variable in class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
-
- temperature - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
-
- temperature - Variable in class etomica.virial.simulations.VirialLJBridge.VirialLJParam
-
- temperature - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
-
- temperature - Variable in class etomica.virial.simulations.VirialLJD.VirialLJParam
-
- temperature - Variable in class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- temperature - Variable in class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
-
- temperature - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
-
- temperature - Variable in class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
-
- temperature - Variable in class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- temperature - Variable in class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
-
- temperature - Variable in class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
-
- temperature - Variable in class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
-
- temperature - Variable in class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
-
- temperature - Variable in class etomica.virial.simulations.VirialRowleyAlcohol.VirialParam
-
- temperature - Variable in class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- temperature - Variable in class etomica.virial.simulations.VirialSW.VirialSWParam
-
- temperature - Variable in class etomica.virial.simulations.VirialTraPPEAlcohol.VirialParam
-
- temperature - Static variable in class org.jmol.script.Token
-
- temperature0 - Variable in class etomica.metastable.LJNVT.LJMCParams
-
- temperatureAverage - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- temperatureDataSource - Variable in class etomica.thermointegration.IntegratorThermodynamicPEvsT
-
- temperatureDisplayTextBox - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- temperatureHistory - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- temperatureK - Variable in class etomica.AlkaneEH.CH4NVT.Param
-
- temperatureK - Variable in class etomica.dielectric.TIP4P_NVT.Param
-
- temperatureK - Variable in class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.VirialParam
-
- temperatureK - Variable in class etomica.virial.simulations.VirialB3C1TIP4Pwater.VirialParam
-
- temperatureK - Variable in class etomica.virial.simulations.VirialB3C2TIP4Pwater.VirialParam
-
- temperatureK - Variable in class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- temperatureK - Variable in class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- temperatureK - Variable in class etomica.virial.simulations.VirialN2.VirialN2Param
-
- temperatureK - Variable in class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- temperatureK - Variable in class etomica.virial.simulations.VirialO2.VirialO2Param
-
- temperatureK - Variable in class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- temperaturePanel - Variable in class etomica.graphics.DeviceThermoSlider
-
- temperaturePump - Variable in class etomica.simulation.prototypes.HSMD2D_noNbr
-
- temperatureSlider - Variable in class etomica.graphics.DeviceThermoSlider
-
- temperatureVec - Variable in class etomica.integrator.IntegratorMD
-
- tempImage - Variable in class etomica.space.BoundaryRectangularPeriodic
-
- tempImage - Variable in class etomica.space.BoundaryRectangularPore
-
- tempImage - Variable in class etomica.space.BoundaryRectangularSlit
-
- template2 - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
-
- template3 - Variable in class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
-
- templateName - Variable in class etomica.potential.PotentialEmul
-
- tempOrientA - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- tempOrientA - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- tempOrientation - Variable in class etomica.integrator.IntegratorRigidIterative
-
- tempOrientation - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- tempOrientB - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- tempOrientB - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- tempQuat - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- tempRotationTensor - Variable in class etomica.integrator.IntegratorRigidIterative
-
- tempSet - Variable in class etomica.virial.B3ForSphericallySymmetricU.DampingParams
-
- tempSlider - Variable in class etomica.modules.adsorption.AdsorptionGraphic
-
- tempSlider - Variable in class etomica.modules.catalysis.CatalysisGraphic
-
- tempSlider - Variable in class etomica.modules.insertion.InsertionGraphic
-
- tempSlider - Variable in class etomica.modules.mu.MuGraphic
-
- tempSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- tempSlider - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- tempSlider - Variable in class etomica.modules.swmd.SwmdGraphic
-
- tempTens - Variable in class etomica.action.BoxInflateDeformable
-
- tempTensInv - Variable in class etomica.action.BoxInflateDeformable
-
- tempTensorkk - Variable in class etomica.potential.EwaldSummation
-
- tempU - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- tempVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- tempVec - Variable in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- tempX - Variable in class etomica.data.history.HistoryScrolling
-
- tempY - Variable in class etomica.data.history.HistoryScrolling
-
- tensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- tensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- tensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- tensor - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DFixedAngle
-
- tensor - Variable in class etomica.models.nitrogen.TestRotationVector
-
- Tensor - Interface in etomica.space
-
Interface for a second-order tensor.
- Tensor1D - Class in etomica.space1d
-
Implementation of a tensor for a 1-dimensional space.
- Tensor1D() - Constructor for class etomica.space1d.Tensor1D
-
Default constructor sets tensor element to zero.
- Tensor1D(double) - Constructor for class etomica.space1d.Tensor1D
-
- Tensor2D - Class in etomica.space2d
-
Implementation of a tensor for a 2-dimensional space.
- Tensor2D() - Constructor for class etomica.space2d.Tensor2D
-
Default constructor sets all tensor elements to zero.
- Tensor2D(double[][]) - Constructor for class etomica.space2d.Tensor2D
-
Constructs tensor with elements set by the given array.
- Tensor3D - Class in etomica.space3d
-
- Tensor3D() - Constructor for class etomica.space3d.Tensor3D
-
Default constructor sets all elements to zero.
- Tensor3D(double[][]) - Constructor for class etomica.space3d.Tensor3D
-
Constructs tensor with elements set by the given array.
- TensorND - Class in etomica.spaceNd
-
Implementation of the 2nd-rank tensor class for arbitrary dimension.
- TensorND(int) - Constructor for class etomica.spaceNd.TensorND
-
Constructs tensor with specified dimension
- TensorND(double[][]) - Constructor for class etomica.spaceNd.TensorND
-
Constructs and initializes tensor to the values given in an array.
- tensorTrans - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- tensorWork - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- test(IAtom) - Method in interface etomica.atom.AtomFilter
-
Returns true if atom is passes test of filter.
- test(IAtom) - Method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.AtomFilterDeviation
-
- test(IAtom) - Method in class etomica.lattice.LatticePlane
-
- test - Variable in class etomica.meam.PotentialCuLREP
-
- test(IAtom) - Method in class etomica.modules.chainequilibrium.AtomFilterChainLength
-
- test(IAtom) - Method in class etomica.modules.droplet.AtomFilterLiquid
-
- test(IAtom) - Method in class etomica.modules.droplet.AtomFilterLiquidAtomic
-
- TestAceticAcidMC3D_NPT - Class in etomica.association.AceticAcid
-
OPLS Acetic Acid Monte Carlo NPT simulation in 3D.
- TestAceticAcidMC3D_NPT(int, double, double, double, long) - Constructor for class etomica.association.AceticAcid.TestAceticAcidMC3D_NPT
-
- TestAceticAcidMC3D_NPT.AceticAcidMCParam - Class in etomica.association.AceticAcid
-
- testBit(int) - Method in interface etomica.graph.model.Bitmap
-
- testBit(int) - Method in class etomica.graph.model.impl.BitmapOfLong
-
TIME = O(1).
- testBit(int) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- TestDifferentImage1DHRAdd - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Output: histogram files of probability that a mode is zero
Calculate free energy of solid
Treats modes as degrees of freedom; uses a MeterDifferentImage to calculate
what happens when an extra mode is added.
- TestDifferentImage1DHRAdd(Space, int, double, int, int[]) - Constructor for class etomica.models.oneDHardRods.TestDifferentImage1DHRAdd
-
- TestDifferentImage1DHRAdd.SimParam - Class in etomica.models.oneDHardRods
-
- TestDifferentImage1DHRSubtract - Class in etomica.models.oneDHardRods
-
MC simulation
1D hard rods
No graphic display
Output: histogram files of probability that a mode is zero
Calculate free energy of solid
Treats modes as degrees of freedom; uses a MeterDifferentImage to calculate
what happens when an extra mode is added.
- TestDifferentImage1DHRSubtract(Space, int, double, int, int[]) - Constructor for class etomica.models.oneDHardRods.TestDifferentImage1DHRSubtract
-
- TestDifferentImage1DHRSubtract.SimParam - Class in etomica.models.oneDHardRods
-
- TestEwaldTIP4PWater - Class in etomica.models.water
-
- TestFiniteDifferenceDerivative - Class in etomica.conjugategradient
-
- TestFiniteDifferenceDerivative() - Constructor for class etomica.conjugategradient.TestFiniteDifferenceDerivative
-
- testflag1 - Static variable in class org.jmol.script.Token
-
- testflag2 - Static variable in class org.jmol.script.Token
-
- testflag3 - Static variable in class org.jmol.script.Token
-
- testflag4 - Static variable in class org.jmol.script.Token
-
- TestHC2YukawaMC3D - Class in etomica.yukawa
-
Hard-core plus two Yukawa fluid Monte-Carlo simulation in 3D
- TestHC2YukawaMC3D() - Constructor for class etomica.yukawa.TestHC2YukawaMC3D
-
- TestHC2YukawaMC3D(int) - Constructor for class etomica.yukawa.TestHC2YukawaMC3D
-
- TestHexane - Class in etomica.models.hexane
-
- TestHexane(Space, double, int, int, int) - Constructor for class etomica.models.hexane.TestHexane
-
- TestHexaneCBMCOnly - Class in etomica.models.hexane
-
- TestHexaneCBMCOnly(Space, int) - Constructor for class etomica.models.hexane.TestHexaneCBMCOnly
-
- TestHexaneFileConfig - Class in etomica.models.hexane
-
- TestHexaneFileConfig(Space, double, int, int, int) - Constructor for class etomica.models.hexane.TestHexaneFileConfig
-
- TestHexaneHarmonic - Class in etomica.models.hexane
-
- TestHexaneHarmonic(Space, int) - Constructor for class etomica.models.hexane.TestHexaneHarmonic
-
- TestHexaneHarmonic.DataProcessorFoo - Class in etomica.models.hexane
-
DataProcessor that sums up the logs of all incoming values
- TestHSMD3D - Class in etomica.tests
-
Simple hard-sphere molecular dynamics simulation in 3D.
- TestHSMD3D(Space, int, int, Configuration) - Constructor for class etomica.tests.TestHSMD3D
-
- TestHSMD3D.SimParams - Class in etomica.tests
-
- TestIGAssociationMC3D_NPT_DoubleSites - Class in etomica.association
-
Simple ideal gas + S-W Association Monte Carlo NPT simulation in 3D.
- TestIGAssociationMC3D_NPT_DoubleSites(int, double, double, double, double, double, int, boolean, long) - Constructor for class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites
-
- TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam - Class in etomica.association
-
- TestLJAssociationMC3D_NPT - Class in etomica.association
-
Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
- TestLJAssociationMC3D_NPT(int, double, double, double, double, long) - Constructor for class etomica.association.TestLJAssociationMC3D_NPT
-
- TestLJAssociationMC3D_NPT - Class in etomica.virial.simulations
-
Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
- TestLJAssociationMC3D_NPT(int, double, double, double, double, long) - Constructor for class etomica.virial.simulations.TestLJAssociationMC3D_NPT
-
- TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam - Class in etomica.association
-
- TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- TestLJAssociationMC3D_NPT_DoubleSites - Class in etomica.association
-
Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
- TestLJAssociationMC3D_NPT_DoubleSites(int, double, double, double, double, double, int, boolean, long) - Constructor for class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites
-
- TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam - Class in etomica.association
-
- TestLJAssociationMC3D_NVTOld - Class in etomica.association
-
Simple Lennard-Jones + S-W Association Monte Carlo NPT simulation in 3D.
- TestLJAssociationMC3D_NVTOld(int, double, double, double, double, long) - Constructor for class etomica.association.TestLJAssociationMC3D_NVTOld
-
- TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam - Class in etomica.association
-
- TestLJGCMC3D - Class in etomica.tests
-
Grand Canonical Lennard-Jones Monte Carlo simulation in 3D.
- TestLJGCMC3D(int, int, Configuration) - Constructor for class etomica.tests.TestLJGCMC3D
-
- TestLJGCMC3D.SimParams - Class in etomica.tests
-
- TestLJMC3D - Class in etomica.tests
-
Simple Lennard-Jones Monte Carlo simulation in 3D.
- TestLJMC3D(int, int, Configuration) - Constructor for class etomica.tests.TestLJMC3D
-
- TestLJMC3D.SimParams - Class in etomica.tests
-
- testMolecule - Variable in class etomica.data.DataSourcePositionedBoltzmannFactor
-
- testMolecule - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- testMoleculeIndex - Variable in class etomica.modules.adsorption.MyMCMove
-
- testMoleculeIndex - Variable in class etomica.modules.dcvgcmd.MyMCMove
-
- TestNonLinearConjugateGradients - Class in etomica.conjugategradient
-
- TestNonLinearConjugateGradients() - Constructor for class etomica.conjugategradient.TestNonLinearConjugateGradients
-
- testOrthoCurvature(Vector[], Vector[]) - Method in class etomica.dimer.IntegratorDimerRT
-
Checks the curvature value at dimer orientation along a vector orthogonal to
lowest curvature mode's (lcm) vector with the lcm's unit vector.
- testPair(Graph, byte, byte, List) - Method in class etomica.graph.property.FFTDecomposition
-
- testPair(Graph, byte, byte, List) - Method in class etomica.graph.property.IsFFT
-
- TestRotationVector - Class in etomica.models.nitrogen
-
- TestRotationVector() - Constructor for class etomica.models.nitrogen.TestRotationVector
-
- TestSetToUHexane - Class in etomica.models.hexane
-
- TestSWChain - Class in etomica.tests
-
Simple square-well chain simulation.
- TestSWChain(Space, int, double, Configuration) - Constructor for class etomica.tests.TestSWChain
-
- TestSWChain.SimParams - Class in etomica.tests
-
- testTransformVector(Vector) - Method in class etomica.space.BoundaryDeformablePeriodic
-
We test the given vector (v) to see if 0.5*v would be transformed by any
of our existing transformVectors.
- TestYukawaMC3D - Class in etomica.yukawa
-
A Yukawa Monte-Carlo simulation in 3D
- TestYukawaMC3D() - Constructor for class etomica.yukawa.TestYukawaMC3D
-
- TestYukawaMC3D(int) - Constructor for class etomica.yukawa.TestYukawaMC3D
-
- TestYukawaMD3D - Class in etomica.yukawa
-
A Yukawa MD Simulation
adapted from HSMD3D simulation prototype.
- TestYukawaMD3D() - Constructor for class etomica.yukawa.TestYukawaMD3D
-
- tetherBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisGraphic
-
- tetherBox - Variable in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic
-
- tetraNum - Variable in class etomica.data.meter.MeterDihedralAngle
-
- textAreaForBonds - Variable in class etomica.modules.clustergenerator.MyApplet
-
- textField - Variable in class etomica.graphics.DeviceBox
-
Object for displaying the value as a text field
- textField - Variable in class etomica.graphics.DeviceSlider
-
To show the values of slider
- TextFormat - Class in org.jmol.util
-
- TextFormat() - Constructor for class org.jmol.util.TextFormat
-
- thermalButtons - Variable in class etomica.graphics.DeviceThermoSlider
-
- thermometer - Variable in class etomica.modules.chainequilibrium.ChainEquilibriumSim
-
- thermometer - Variable in class etomica.modules.dcvgcmd.DCVGCMD
-
- thermometer - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- thermometer - Variable in class etomica.modules.reactionequilibrium.ReactionEquilibrium
-
- thermostat - Variable in class etomica.integrator.IntegratorMD
-
- thermostatActions - Variable in class etomica.normalmode.IntegratorHardMDMC
-
- thermostatCount - Variable in class etomica.integrator.IntegratorMD
-
- thermostatInterval - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- thermostatInterval - Variable in class etomica.integrator.IntegratorMD
-
- thermostatNoDrift - Variable in class etomica.integrator.IntegratorMD
-
- thermostatting - Variable in class etomica.integrator.IntegratorMD
-
- thermostatType - Variable in class etomica.modules.render.RenderMD.RenderMDParam
-
- THETA - Variable in class etomica.dimer.IntegratorDimerMin
-
- THETA - Variable in class etomica.dimer.IntegratorDimerRT
-
- theta - Variable in class etomica.normalmode.HSDimerNPT
-
- theta - Variable in class etomica.potential.P2QChemInterpolated
-
- theta - Variable in class etomica.virial.MCMoveClusterRotateMoleculeMulti
-
- theta - Static variable in class org.jmol.script.Token
-
- thetaFrac - Variable in class etomica.normalmode.HSDimerNPT.HSMD3DParameters
-
- thetaFrac - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecularOriented
-
- thetaSlider - Variable in class etomica.modules.sam.SamGraphic
-
- THETAstar - Variable in class etomica.dimer.IntegratorDimerMin
-
- THETAstar - Variable in class etomica.dimer.IntegratorDimerRT
-
- THETAstarstar - Variable in class etomica.dimer.IntegratorDimerRT
-
- thirdAxis - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- thirdAxis - Variable in class etomica.association.BiasVolumeAceticAcid
-
- thisBox(Box) - Static method in class etomica.util.Debug
-
Checks whether the given box is of debugging interest
- threadCalculate - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- threadCalculate - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- threadList - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- threadList - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- threadNumber - Variable in class etomica.threaded.atom.PotentialMasterListWorker
-
- threadNumber - Variable in class etomica.threaded.domain.PotentialMasterListWorker
-
- ThreadsMD - Class in etomica.threads
-
- ThreadsMD(int, int, int, int, double, double[][], double[][], double[][], AtomDecompositionMD) - Constructor for class etomica.threads.ThreadsMD
-
- threej(int, int, int, int, int, int) - Static method in class etomica.potential.P2O2Bartolomei
-
- threesqrt3a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
-
- threesqrt3a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
-
- threshold - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.AtomFilterDeviation
-
- threshold - Variable in class etomica.graphics.DeviceDelaySlider
-
- thresholdS - Variable in class etomica.freeenergy.npath.ConfigFromFileLAMMPS.ConfigFromFileLAMMPSParam
-
- ti - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- TIFF - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- TIFF_CODE - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- TIFF_EXTENSION - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- TIFF_STR - Static variable in class etomica.graph.view.rasterizer.DestinationType
-
- Tij - Variable in class etomica.models.co2.PNCO2GCPM
-
- Tij - Variable in class etomica.models.water.PNWaterGCPM
-
- tilt - Variable in class etomica.math.numerical.AkimaSplineSmootherApp.PlotAction
-
- tilt - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp.PlotAction
-
- time - Variable in class etomica.graph.traversal.Biconnected
-
- time - Variable in class etomica.integrator.IntegratorAnalytic.AtomTimeAction
-
- Time - Class in etomica.units.dimensions
-
Dimension for all units of time.
- time() - Method in class etomica.units.systems.CGS
-
- time() - Method in class etomica.units.systems.LJ
-
- time() - Method in class etomica.units.systems.MKS
-
- time() - Method in class etomica.units.systems.UnitSystem.Sim
-
- time() - Method in class etomica.units.systems.UnitSystem
-
- TIMEDBALL - Static variable in class g3dsys.control.G3DSys
-
- TimeOptionHandler() - Constructor for class etomica.graph.view.rasterizer.Main.TimeOptionHandler
-
- timer - Variable in class etomica.graphics.DisplayTimer
-
- times(Complex) - Method in class etomica.math.Complex
-
Complex multiplication (doesn't change this Complex number).
- times(Rational) - Method in class etomica.math.Rational
-
Returns a new Rational instance, which is the result of multiplying this
Rational by the given Rational.
- timeStep - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- timeStep - Variable in class etomica.integrator.IntegratorMD
-
- timeStep - Variable in class etomica.modules.render.RenderMD.RenderMDParam
-
- timlim - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- Tin - Class in etomica.chem.elements
-
Class for the Tin element.
- Tin(String) - Constructor for class etomica.chem.elements.Tin
-
- Tin(String, double) - Constructor for class etomica.chem.elements.Tin
-
- TIP4P_NVT - Class in etomica.dielectric
-
Canonical ensemble Monte Carlo simulation (NVT)
dielectric constant (epsilon)
TIP4P water
- TIP4P_NVT(Space, int, double, double, double, double) - Constructor for class etomica.dielectric.TIP4P_NVT
-
- TIP4P_NVT.DipoleSourceTIP4PWater - Class in etomica.dielectric
-
- TIP4P_NVT.Param - Class in etomica.dielectric
-
- tKelvin - Variable in class etomica.potential.P2WaterPotentialsJankowski
-
- tmp - Variable in class etomica.overlap.DataOverlap
-
- tmpAtomicTensor3 - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
-
- tmpDrr - Variable in class etomica.models.water.P2Water4PSoft
-
- tmpDrr1 - Variable in class etomica.normalmode.LatticeSumMolecularCrystal
-
- tmpSecondD - Variable in class etomica.models.water.P2Water4PSoft
-
- tmpTensor - Variable in class etomica.models.water.P2Water4PSoft
-
- toArray() - Method in class etomica.atom.AtomArrayList
-
- toArray() - Method in class etomica.graph.model.GraphList
-
- toArray(T[]) - Method in class etomica.graph.model.GraphList
-
- toArray() - Method in class etomica.molecule.MoleculeArrayList
-
- toArray() - Method in interface etomica.space.Tensor
-
Returns tensor in a new array, writing elements row-wise.
- toArray() - Method in interface etomica.space.Vector
-
- toArray() - Method in class etomica.space1d.Tensor1D
-
- toArray() - Method in class etomica.space2d.Tensor2D
-
Returns tensor in an array, writing rowwise, i.e., in order xx, xy, yx, yy.
- toArray() - Method in class etomica.space3d.Tensor3D
-
Returns tensor in a new array, writing elements row-wise, i.e.: xx, xy, xz, yx, yy, yz, zx, zy, zz;
- toArray() - Method in class etomica.spaceNd.TensorND
-
- toArray() - Method in class org.jmol.script.ScriptVariable
-
- toAtomLeafArray() - Method in class etomica.atom.AtomArrayList
-
- toAxisAngle4f() - Method in class org.jmol.util.Quaternion
-
- toBytes(int, int) - Method in class org.jmol.util.StringXBuilder
-
simple byte conversion not allowing for unicode.
- toCanonical - Static variable in class org.jmol.util.BoxInfo
-
- toE(ClusterDiagram) - Static method in class etomica.virial.cluster.ClusterOperations
-
Returns an array of cluster diagrams with all e-bonds representing
the same sum of diagrams as the given f-bond cluster.
- toE(ClusterDiagram[]) - Static method in class etomica.virial.cluster.ClusterOperations
-
Returns an array of cluster diagrams with all e-bonds representing
the same sum of diagrams as the given f-bond clusters.
- toFString(int) - Method in class etomica.veos.bigdecimal.Rational
-
Return a string in floating point format.
- toggle() - Method in class etomica.graphics.DeviceCheckBox
-
Toggles the state of the button (true to false, false to true).
- toggleAction - Variable in class etomica.graphics.DeviceToggleButton
-
- toggleInPlace(BitSet, BitSet) - Static method in class org.jmol.util.BitSetUtil
-
a perhaps curious method:
b is a reference set, perhaps all atoms in a certain molecule a is the
working set, perhaps representing all displayed atoms
For each set bit in b: a) if a is also set, then clear a's bit UNLESS b) if
a is not set, then add to a all set bits of b
Thus, if a equals b --> clear all if a is a subset of b, then --> b if b is
a subset of a, then --> a not b if a only intersects with b, then --> a or
b if a does not intersect with b, then a or b
In "toggle" mode, when you click on any atom of the molecule, you want
either:
(a) all the atoms in the molecule to be displayed if not all are already
displayed, or
(b) the whole molecule to be hidden if all the atoms of the molecule are
already displayed.
- toIfactor(int) - Method in class etomica.veos.bigdecimal.Factorial
-
Compute the factorial of the non-negative integer.
- toInt() - Method in class etomica.graph.view.rasterizer.DestinationType
-
- toJSON(String, Object) - Static method in class org.jmol.util.Escape
-
- tok - Variable in class org.jmol.script.Token
-
- tokAttr(int, int) - Static method in class org.jmol.script.Token
-
- tokAttrOr(int, int, int) - Static method in class org.jmol.script.Token
-
- Token - Class in org.jmol.script
-
- Token() - Constructor for class org.jmol.script.Token
-
- Token(int) - Constructor for class org.jmol.script.Token
-
- tokenAnd - Static variable in class org.jmol.script.Token
-
- tokenAND - Static variable in class org.jmol.script.Token
-
- tokenAndFALSE - Static variable in class org.jmol.script.Token
-
- tokenComma - Static variable in class org.jmol.script.Token
-
- tokenConnected - Static variable in class org.jmol.script.Token
-
- tokenExpressionBegin - Static variable in class org.jmol.script.Token
-
- tokenExpressionEnd - Static variable in class org.jmol.script.Token
-
- tokenLeftParen - Static variable in class org.jmol.script.Token
-
- tokenOpIf - Static variable in class org.jmol.script.Token
-
- tokenOr - Static variable in class org.jmol.script.Token
-
- tokenOrTRUE - Static variable in class org.jmol.script.Token
-
- tokenRightParen - Static variable in class org.jmol.script.Token
-
- tol - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
-
- tol - Variable in class etomica.virial.ClusterWheatleySoft
-
- tol - Variable in class etomica.virial.ClusterWheatleySoftBD
-
- tol - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- tol - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- tolerance - Variable in class etomica.action.ActionMinimizeEnergy
-
- tolerance - Variable in class etomica.data.histogram.HistogramDiscrete
-
- tolerance - Variable in class etomica.models.nitrogen.FindTransitionTemperature
-
- tolerance - Variable in class etomica.models.nitrogen.MinimizeBetaNitrogenTranslationDOF
-
- tolerance - Variable in class etomica.modules.interfacial.FitTanh
-
- tolerance - Variable in class etomica.normalmode.SoftSphereSolidEOS
-
- tolerance - Variable in class etomica.surfacetension.FitTanh
-
- tolf - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- tolr - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- toMoleculeArray() - Method in class etomica.molecule.MoleculeArrayList
-
- toNumberString() - Method in interface etomica.graph.model.Bitmap
-
Returns a string for the integer represented by this bitmap
- toNumberString() - Method in class etomica.graph.model.impl.AbstractBitmap
-
- toolbar - Variable in class etomica.graphics.SimulationPanel
-
- toolbarPanel - Variable in class etomica.graphics.SimulationPanel
-
- TOP - Static variable in class etomica.graphics.DisplayBox
-
- TOP - Static variable in class etomica.graphics.DisplayPolytope
-
- TOP - Static variable in class etomica.math.Gamma
-
- toPattern() - Method in class etomica.util.ScientificFormat
-
- TOPEXP - Static variable in class etomica.math.Gamma
-
- toPixels() - Method in class etomica.units.Pixel
-
- toPoint4f() - Method in class org.jmol.util.Quaternion
-
- topPadding - Variable in class etomica.interfacial.ConfigurationLammps
-
- toPString() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Print as a polyomial in x.
- topWall - Variable in class etomica.interfacial.MeterWallForce
-
- toRational() - Method in class etomica.veos.bigdecimal.BigSurd
-
Convert to a rational value if possible
- toRatPoly() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Translate into a RatPoly copy.
- toReadable(String, Object) - Static method in class org.jmol.util.Escape
-
- torque - Variable in class etomica.action.ActionMinimizeEnergy.MyForceTorque
-
- torque() - Method in class etomica.action.ActionMinimizeEnergy.MyForceTorque
-
- torque() - Method in interface etomica.integrator.Integrator.Torquable
-
- torque - Variable in class etomica.integrator.IntegratorRigidIterative.MoleculeAgent
-
- torque() - Method in class etomica.integrator.IntegratorRigidIterative.MoleculeAgent
-
- torque - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.MoleculeAgent
-
- torque() - Method in class etomica.integrator.IntegratorRigidMatrixIterative.MoleculeAgent
-
- torque - Variable in class etomica.models.co2.P2CO2H2OWheatley
-
- torque - Variable in class etomica.models.co2.P2CO2Hellmann
-
- torque - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- torque - Variable in class etomica.models.water.P2Water3PSoft
-
- torque - Variable in class etomica.models.water.P2Water4PSoft
-
- torque - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- torque - Variable in class etomica.potential.P2HSDipole
-
- torque - Variable in class etomica.potential.P2LJDipole
-
- torque - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion.MoleculeAgent
-
- torque - Variable in class etomica.rotation.P2LJDipole
-
- torqueF - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- torqueSum - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- torqueSum - Variable in class etomica.integrator.IntegratorRigidIterative
-
- torqueSum - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- torqueSum - Variable in class etomica.modules.rosmosis.ReverseOsmosisWater
-
- torqueSum - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- torsionPotential - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- torsionPotential - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- toSim(double) - Method in class etomica.units.CompoundUnit
-
- toSim(double) - Method in class etomica.units.PrefixedUnit
-
Takes the given value in class units (considering prefix) and converts it to simulation units.
- toSim(double) - Method in class etomica.units.SimpleUnit
-
Takes the given value in class units and converts it to simulation units.
- toSim(double) - Method in class etomica.units.systems.LJ.LJUnit
-
- toSim(double) - Method in interface etomica.units.Unit
-
Takes the given value in class units (considering prefix) and converts it to simulation units.
- toSpherical(Vector, double[]) - Static method in class etomica.math.geometry.coordinate.CoordinateConverter
-
- toString() - Method in class etomica.action.activity.Controller
-
- toString() - Method in class etomica.atom.Atom
-
Returns a string formed by concatenating the signature of this atom
to a string that identifies it as a species master, species agent,
molecule, group, or (leaf) atom.
- toString() - Method in class etomica.atom.AtomArrayList
-
- toString() - Method in class etomica.atom.AtomPair
-
- toString() - Method in class etomica.atom.AtomsetArray
-
- toString() - Method in class etomica.atom.AtomSetSinglet
-
- toString() - Method in class etomica.box.Box
-
- toString() - Method in class etomica.data.AccumulatorAverage.StatType
-
- toString() - Method in class etomica.data.AccumulatorAverageBlockless.StatType
-
- toString() - Method in class etomica.data.AccumulatorAverageBlocklessSlim.StatType
-
- toString() - Method in class etomica.data.DataAccumulator
-
- toString() - Method in class etomica.data.DataInfo
-
Returns "label (dimension)", where label and dimension are the values
held by this instance.
- toString() - Method in interface etomica.data.IDataInfo
-
Returns "label (dimension)", where label and dimension are the values
held by this instance.
- toString() - Method in class etomica.data.types.DataDouble
-
Returns a string formed from the dataInfo label and this value.
- toString() - Method in class etomica.data.types.DataDoubleArray
-
Returns a string formed from the dataInfo label and the array values.
- toString() - Method in class etomica.data.types.DataDoubleBDArray
-
Returns a string formed from the dataInfo label and the array values.
- toString() - Method in class etomica.data.types.DataGroup
-
Returns a string formed from the encapsulated data objects.
- toString() - Method in class etomica.data.types.DataTensor
-
Returns a string formed from the dataInfo label and the tensor values.
- toString() - Method in class etomica.data.types.DataVector
-
Returns a string formed from the dataInfo label and the vector values.
- toString() - Method in class etomica.graph.isomorphism.NodePair
-
- toString() - Method in class etomica.graph.model.GraphList
-
- toString() - Method in class etomica.graph.model.impl.AbstractBitmap
-
- toString() - Method in class etomica.graph.model.impl.CoefficientImpl
-
- toString() - Method in class etomica.graph.model.impl.EdgeImpl
-
- toString() - Method in class etomica.graph.model.impl.GraphImpl
-
- toString() - Method in class etomica.graph.model.impl.MetadataImpl
-
- toString() - Method in class etomica.graph.model.impl.NodeImpl
-
- toString() - Method in class etomica.graph.view.rasterizer.DestinationType
-
- toString(String[]) - Method in class etomica.graph.view.rasterizer.Main
-
- toString() - Method in class etomica.graph.view.rasterizer.SVGConverterFileSource
-
- toString() - Method in class etomica.graph.view.rasterizer.SVGConverterURLSource
-
- toString() - Method in class etomica.graphics.Display
-
Overrides the Object class toString method to have it return the output
of getName
- toString() - Method in class etomica.integrator.IntegratorHard.Agent
-
- toString() - Method in class etomica.integrator.mcmove.MCMove
-
- toString() - Method in class etomica.integrator.mcmove.MCMoveBox
-
- toString() - Method in class etomica.lattice.crystal.PrimitiveBcc
-
- toString() - Method in class etomica.lattice.crystal.PrimitiveCubic
-
- toString() - Method in class etomica.lattice.crystal.PrimitiveFcc
-
- toString() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- toString() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- toString() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- toString() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- toString() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
- toString() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- toString() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- toString() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- toString() - Method in class etomica.lattice.LatticeCubicBcc
-
Returns "Bcc".
- toString() - Method in class etomica.lattice.LatticeCubicDiamond
-
Returns "Diamond".
- toString() - Method in class etomica.lattice.LatticeCubicFcc
-
Returns "Fcc".
- toString() - Method in class etomica.lattice.LatticeCubicSimple
-
Returns "Simple cubic".
- toString() - Method in class etomica.lattice.LatticeHcp
-
- toString() - Method in class etomica.lattice.LatticeHcp4
-
- toString() - Method in class etomica.lattice.LatticeOrthorhombicHexagonal
-
Returns "OrthorhombicHexagonal".
- toString() - Method in class etomica.math.Complex
-
String representation of this Complex number.
- toString() - Method in class etomica.math.DoubleRange
-
Returns String of the form [min,max]
- toString() - Method in class etomica.math.geometry.Point
-
- toString() - Method in class etomica.math.geometry.Polytope
-
- toString() - Method in class etomica.math.Quaternion
-
Returns the string representation of the Quaternion q
- toString() - Method in class etomica.math.Rational
-
- toString() - Method in class etomica.models.hexane.PrimitiveHexane
-
- toString() - Method in class etomica.modules.pistoncylinder.ModifierPistonPressure
-
- toString() - Method in class etomica.modules.pistoncylinder.PistonCylinderGraphic.ModifierAtomDiameter
-
- toString() - Method in class etomica.modules.rosmosis.ReverseOsmosisGraphic.ModifierAtomDiameter
-
- toString() - Method in class etomica.modules.rosmosis.ReverseOsmosisWaterGraphic.ModifierAtomDiameter
-
- toString() - Method in class etomica.modules.swmd.SwmdGraphic.ModifierAtomDiameter
-
- toString() - Method in class etomica.molecule.Molecule
-
Returns a string formed by concatenating the signature of this atom
to a string that identifies it as a molecule.
- toString() - Method in class etomica.molecule.MoleculePair
-
- toString() - Method in class etomica.molecule.MoleculesetArray
-
- toString() - Method in class etomica.molecule.MoleculeSetSinglet
-
- toString() - Method in class etomica.normalmode.MCMoveRotateMoleculePhiTheta
-
- toString() - Method in class etomica.space1d.Vector1D
-
- toString() - Method in class etomica.space2d.Tensor2D
-
- toString() - Method in class etomica.space2d.Vector2D
-
- toString() - Method in class etomica.space3d.Tensor3D
-
- toString() - Method in class etomica.space3d.Vector3D
-
- toString() - Method in class etomica.spaceNd.TensorND
-
- toString() - Method in class etomica.spaceNd.VectorND
-
- toString() - Method in class etomica.units.dimensions.Dimension
-
- toString() - Method in enum etomica.units.Prefix
-
- toString() - Method in class etomica.units.PrefixedUnit
-
- toString() - Method in class etomica.units.SimpleUnit
-
- toString() - Method in enum etomica.util.Constants.CompassDirection
-
- toString() - Method in class etomica.util.TreeLinker
-
- toString() - Method in class etomica.veos.bigdecimal.BigComplex
-
Human-readable Fortran-type display
- toString(MathContext) - Method in class etomica.veos.bigdecimal.BigComplex
-
Human-readable Fortran-type display
- toString() - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Print as a comma-separated list of coefficients.
- toString() - Method in class etomica.veos.bigdecimal.BigSurd
-
Return a string in the format (number/denom)*()^(1/2).
- toString() - Method in class etomica.veos.bigdecimal.BigSurdVec
-
Return a string in the format (number/denom)*()^(1/2).
- toString() - Method in class etomica.veos.bigdecimal.Ifactor
-
Convert to printable format
- toString() - Method in class etomica.veos.bigdecimal.Rational
-
Return a string in the format number/denom.
- toString() - Method in class etomica.virial.cluster.ClusterDiagram
-
- toString() - Method in class etomica.virial.ClusterBonds
-
- toString() - Method in class etomica.virial.IntSet
-
- toString() - Method in class etomica.virial.MCMoveClusterAtomQ
-
- toString() - Method in class org.jmol.script.ScriptVariable
-
- toString() - Method in class org.jmol.script.Token
-
- toString() - Method in class org.jmol.util.AxisAngle4f
-
Returns a string that contains the values of this AxisAngle4f.
- toString() - Method in class org.jmol.util.BitSet
-
Returns a string representation of this bit set.
- toString() - Method in class org.jmol.util.Matrix3f
-
Returns a string that contains the values of this Matrix3f.
- toString() - Method in class org.jmol.util.Matrix4f
-
Returns a string that contains the values of this Matrix4f.
- toString() - Method in class org.jmol.util.Quadric
-
- toString() - Method in class org.jmol.util.Quaternion
-
Java axisAngle / plane / Point4f format
all have the format {x y z w}
so we go with that here as well
- toString() - Method in class org.jmol.util.Rgb16
-
- toString() - Method in class org.jmol.util.StringXBuilder
-
- toString() - Method in class org.jmol.util.Tuple3f
-
Returns a string that contains the values of this Tuple3f.
- toString() - Method in class org.jmol.util.Tuple3i
-
Returns a string that contains the values of this Tuple3i.
- toString() - Method in class org.jmol.util.Tuple4f
-
Returns a string that contains the values of this Tuple4f.
- toStringArray(Object[]) - Static method in class etomica.util.Strings
-
Takes an array of objects and converts them to an array of strings,
with each string given by the object's toString method.
- toSVG(int) - Method in interface etomica.graph.model.Graph
-
- toSVG(int) - Method in class etomica.graph.model.impl.GraphImpl
-
- tot - Variable in class etomica.virial.ClusterICPYC
-
- total - Static variable in class etomica.graph.isomorphism.Match
-
- total - Static variable in class etomica.models.oneDHardRods.MeterOverlapSameGaussian1D
-
- total - Variable in class etomica.modules.chainequilibrium.MeterConversion
-
- total - Variable in class etomica.virial.ClusterWheatleyHS
-
- total - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- total - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- totalAtomCount - Variable in class etomica.modules.entropylottery.DataSourceProbabilityDensity
-
- totalBlockSum - Variable in class etomica.data.AccumulatorAverageCollapsing
-
- totalCells - Variable in class etomica.threaded.domain.NeighborCellManagerThreaded
-
- totalChildCount - Variable in class etomica.species.SpeciesSpheresHetero
-
- totalCount - Variable in class etomica.data.histogram.HistogramDiscrete
-
- totalCount - Variable in class etomica.virial.MCMoveClusterAtomHSRing
-
- totalCount - Variable in class etomica.virial.MeterVirialBDBin
-
- totalCount - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- totalCount - Variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- totalCount - Variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- totalCount - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- totalCount - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- totalDeleteCandidateTimes - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy
-
- totalDeleteCandidateTimes - Variable in class etomica.integrator.mcmove.MCMoveInsertDeleteVacancy
-
- totalMass - Variable in class etomica.models.water.PNWaterGCPM
-
- totalMolecules - Variable in class etomica.virial.MayerFunctionThreeBody
-
- totalNCluster - Variable in class etomica.modules.clustergenerator.MyApplet
-
- totalSteps - Variable in class etomica.data.DataPumpListenerPow
-
- totalSum - Variable in class etomica.data.histogram.HistogramNotSoSimple
-
- totalSumBlockSq - Variable in class etomica.data.AccumulatorAverageCollapsing
-
- totalSumSquare - Variable in class etomica.data.AccumulatorAverageCollapsing
-
- totcount - Variable in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- totcount - Variable in class etomica.virial.ClusterWheatleyMultibodyDerivatives
-
- totcount - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- totNumSubSteps - Variable in class etomica.overlap.IntegratorOverlap
-
- totPCore - Variable in class etomica.virial.MCMoveClusterAtomChainHSTail
-
- totSqErr - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- totTime - Variable in class etomica.overlap.IntegratorOverlap
-
- toWriteFile - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- Tprod(Vector, Vector, Vector, double) - Method in class etomica.models.water.P2WaterSzalewicz
-
Calculate the vector V resulting from the action
of the dipole propagator tensor T_ij on U
Ri, Rj - position vectors of molecules i and j, respectively
rij = |Ri - Rj|^(-3)
- trace() - Method in interface etomica.space.Tensor
-
- trace() - Method in class etomica.space1d.Tensor1D
-
- trace() - Method in class etomica.space2d.Tensor2D
-
- trace() - Method in class etomica.space3d.Tensor3D
-
- trace() - Method in class etomica.spaceNd.TensorND
-
- trace - Static variable in class org.jmol.script.Token
-
- tracealpha - Static variable in class org.jmol.script.Token
-
- tracker - Variable in class etomica.config.ConformationChain2D
-
- trajectory - Static variable in class org.jmol.script.Token
-
- transcode(SVGConverterSource, File, Transcoder) - Method in class etomica.graph.view.rasterizer.SVGConverter
-
Converts the input image to the result image.
- transform() - Method in class etomica.math.numerical.FastFourierTransform
-
Forward Transformation of discrete data sets
- transform(Vector) - Method in interface etomica.space.Tensor
-
Applies the given tensor transformation to this vector, replacing its
elements with the transformed values.
- transform(Vector) - Method in class etomica.space1d.Tensor1D
-
- transform(Vector) - Method in class etomica.space2d.Tensor2D
-
- transform(Vector) - Method in class etomica.space3d.Tensor3D
-
- transform(Vector) - Method in class etomica.spaceNd.TensorND
-
- transform(IMolecule, double) - Method in class etomica.virial.MCMoveClusterAngleBend
-
- transform(IMolecule, double) - Method in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- transform(Tuple3f) - Method in class org.jmol.util.Matrix3f
-
- transform(Point3f) - Method in class org.jmol.util.Matrix4f
-
Transforms the point parameter with this Matrix4f and places the result
back into point.
- transform(Vector3f) - Method in class org.jmol.util.Quaternion
-
- transform2(Tuple3f, Tuple3f) - Method in class org.jmol.util.Matrix3f
-
Transform the vector vec using this Matrix3f and place the result into
vecOut.
- transform2(Point3f, Point3f) - Method in class org.jmol.util.Matrix4f
-
Transforms the point parameter with this Matrix4f and places the result
into pointOut.
- transform4(Tuple4f) - Method in class org.jmol.util.Matrix4f
-
Transform the vector vec using this Matrix4f and place the result back into
vec.
- transformFunction - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- TransformManager - Class in g3dsys.control
-
- transformP2(Tuple3f, Tuple3f) - Method in class org.jmol.util.Quaternion
-
- transformPoints(List<Point3f>, Matrix4f, Point3f) - Static method in class org.jmol.util.Measure
-
- transformPt(Point3f) - Method in class org.jmol.util.Quaternion
-
- transformT2(Tuple4f, Tuple4f) - Method in class org.jmol.util.Matrix4f
-
Transform the vector vec using this Matrix4f and place the result into
vecOut.
- transformV(Vector3f) - Method in class org.jmol.util.Matrix4f
-
Transforms the normal parameter by this transform and places the value back
into normal.
- transformV2(Vector3f, Vector3f) - Method in class org.jmol.util.Matrix4f
-
Transforms the normal parameter by this Matrix4f and places the value into
normalOut.
- transformVectors - Variable in class etomica.space.BoundaryDeformablePeriodic
-
- translate - Static variable in class org.jmol.script.Token
-
- translateBy - Variable in class etomica.integrator.IntegratorRigidIterative
-
- translateBy - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
-
- translateBy - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- translateBy - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- translateBy - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- translateBy - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- translateBy - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- translateBy - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- translateBy - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- translateBy - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- translateBy - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- translateBy - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- translateBy - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- translateBy - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- translateBy - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- translateBy - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- translateDimerQuickmin() - Method in class etomica.dimer.IntegratorDimerRT
-
Moves the dimer along the lowest curvature mode of the energy surface, Quickmin style.
- translateMonomerB() - Method in class etomica.action.IntegratorDimerApproach
-
- translateTo - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- translateTo - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- translation(double[], double[], Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM
-
- translation(double[], double[], double[], Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPM4Pt
-
- translation - Static variable in class org.jmol.script.Token
-
- translation2Mol(int, double[], Box) - Method in class etomica.virial.ConfigurationClusterAceticAcid
-
- translation3Mol(double[], double[], Box) - Method in class etomica.virial.ConfigurationClusterAceticAcid
-
- translationRandom(IMolecule, Box) - Method in class etomica.virial.ConfigurationClusterAceticAcid
-
- translationTetramer(double[], double[], double[], Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- translationTrimer(double[], double[], Box) - Method in class etomica.virial.ConfigurationClusterWertheimGCPMDirectSampling
-
- translationVector - Variable in class etomica.action.BoxInflateAnisotropic
-
- translationVector - Variable in class etomica.action.IntegratorDimerApproach
-
- translationVector() - Method in class etomica.action.IntegratorDimerApproach
-
- translationVector - Variable in class etomica.association.MCMoveDimer
-
- translationVector - Variable in class etomica.association.MCMoveSmer
-
- translationVector - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- translationVector - Variable in class etomica.integrator.mcmove.MCMoveAtom
-
- translationVector - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- translationVector - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- translationVector - Variable in class etomica.modules.entropylottery.MCMoveAtomAdjacent
-
- translationVector - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- translationVector - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- translationVector - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- translationVector - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- translationVectors - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- translationVectors - Variable in class etomica.virial.MCMoveClusterAtomDiscrete
-
- translationVectors - Variable in class etomica.virial.MCMoveClusterAtomMulti
-
- translationVectors - Variable in class etomica.virial.MCMoveClusterMoleculeMulti
-
- translationVectors - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- translationVectors - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- translationVectors - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- translationVectors - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- translator - Variable in class etomica.action.BoxInflate
-
- translator - Variable in class etomica.integrator.IntegratorRigidIterative
-
- translator - Variable in class etomica.integrator.IntegratorRigidMatrixIterative.BoxImposePbcMolecule
-
- translator - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- translator - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- translator - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- translator - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- translucencyMask - Variable in class org.jmol.g3d.Graphics3D
-
- translucent - Static variable in class org.jmol.script.Token
-
- TRANSLUCENT_50 - Static variable in class org.jmol.util.Colix
-
- TRANSLUCENT_MASK - Static variable in class org.jmol.util.Colix
-
- TRANSLUCENT_SCREENED - Static variable in class org.jmol.util.Colix
-
- TRANSLUCENT_SHIFT - Static variable in class org.jmol.util.Colix
-
- translucentCoverOnly - Variable in class org.jmol.g3d.Graphics3D
-
- TRANSPARENT - Static variable in class org.jmol.util.Colix
-
- transpose() - Method in interface etomica.space.Tensor
-
Performs a transpose operation on this tensor, replacing each element ab by its counterpart element ba
- transpose() - Method in class etomica.space1d.Tensor1D
-
- transpose() - Method in class etomica.space2d.Tensor2D
-
- transpose() - Method in class etomica.space3d.Tensor3D
-
- transpose() - Method in class etomica.spaceNd.TensorND
-
- transpose() - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to its transpose.
- transpose() - Method in class org.jmol.util.Matrix4f
-
Sets the value of this matrix to its transpose.
- transposed - Variable in class etomica.graphics.DisplayTable
-
- transposeM(Matrix3f) - Method in class org.jmol.util.Matrix3f
-
Sets the value of this matrix to the transpose of the argument matrix
- transVect - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- tRatio - Variable in class etomica.virial.MeterVirialBDBin
-
- tRatio - Static variable in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- tRatio - Static variable in class etomica.virial.MeterVirialBinMultiThreaded
-
- tRatio - Static variable in class etomica.virial.MeterVirialEBinMultiThreaded
-
- tRatio - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- tRatio - Variable in class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
-
- tRatio - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- tRatio - Variable in class etomica.virial.simulations.VirialSQWRecalcSmallMem.VirialHSParam
-
- Traversal - Interface in etomica.graph.traversal
-
This interface generalizes algorithms that traverse the nodes of a graph.
- TraversalVisitor - Interface in etomica.graph.traversal
-
- traverseAll(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal
-
The only reason to override this method is to change the node choice before
traversing each component, or to traverse more complex components such as
biconnected, K-connected, etc.
- traverseAll(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.BiconectedNodalPoint
-
A variation of BCTraversal that only traverses connected components starting with
field nodes.
- traverseAll(Graph, TraversalVisitor) - Method in class etomica.graph.traversal.Biconnected
-
- traverseAll(Graph, TraversalVisitor) - Method in interface etomica.graph.traversal.Traversal
-
Traverses all components of the graph, starting at an arbitrary node for each
component, and returns the total number of components traversed.
- traverseBCC(byte, Graph, boolean) - Method in class etomica.graph.traversal.Biconnected
-
- traverseComponent(byte, Graph) - Method in class etomica.graph.traversal.AbstractTraversal
-
- traverseComponent(byte, Graph, TraversalVisitor) - Method in class etomica.graph.traversal.AbstractTraversal
-
There should be no reason to override this method.
- traverseComponent(byte, Graph) - Method in class etomica.graph.traversal.Biconnected
-
- traverseComponent(byte, Graph) - Method in class etomica.graph.traversal.BreadthFirst
-
- traverseComponent(byte, Graph) - Method in class etomica.graph.traversal.DepthFirst
-
- traverseComponent(byte, Graph, TraversalVisitor) - Method in interface etomica.graph.traversal.Traversal
-
Traverses a single component of the graph starting at the designated node.
- TREE - Static variable in class etomica.virial.simulations.VirialHS.VirialHSParam
-
- TREE - Static variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- TREE - Static variable in class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- TREE - Static variable in class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- TREE - Static variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- TREE_CHAIN - Static variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- TREE_CHAIN_RING - Static variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- treeFrac - Variable in class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- TreeLinker - Class in etomica.util
-
Linker used in the binary tree TreeList.
- TreeLinker(Object) - Constructor for class etomica.util.TreeLinker
-
Constructor throws exception if given atom is null.
- TreeList - Class in etomica.util
-
TreeList is a generic binary tree structure made up of TreeLinkers.
- TreeList() - Constructor for class etomica.util.TreeList
-
- trialCount - Variable in class etomica.virial.MCMoveClusterRotateMolecule3D
-
- trialNotify() - Method in class etomica.virial.BoxCluster
-
Inform the box that a trial move has been made so it can update
the coordinate pairs.
- trialP - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- Triangle - Class in g3dsys.images
-
Class for drawing triangles (possibly making up a polygon)
- Triangle(G3DSys, short, Point3f, Point3f, Point3f) - Constructor for class g3dsys.images.Triangle
-
- TriangleData - Class in org.jmol.util
-
- TriangleData() - Constructor for class org.jmol.util.TriangleData
-
- triangles - Static variable in class org.jmol.script.Token
-
- triangleTable2 - Static variable in class org.jmol.util.TriangleData
-
- trim - Static variable in class org.jmol.script.Token
-
- trim(String, String) - Static method in class org.jmol.util.TextFormat
-
- trimerPotential - Variable in class etomica.association.MCMoveSmer
-
- trimerPotential - Variable in class etomica.association.MCMoveSmerRotate
-
- trimToSize() - Method in class etomica.atom.AtomArrayList
-
- trimToSize() - Method in class etomica.molecule.MoleculeArrayList
-
- tripletDone - Variable in class etomica.virial.PotentialCommonAtomic
-
- tripletDone - Variable in class etomica.virial.PotentialGroup3PI
-
- tripletId(int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagrams
-
Returns the triplet ID for the given indices (id0, id1, id2) and given
number of molecules (n).
- tripletId(int, int, int, int) - Static method in class etomica.virial.cluster.VirialDiagramsPT
-
Returns the triplet ID for the given indices (id0, id1, id2) and given
number of molecules (n).
- TripletInnerSequential - Class in etomica.atom.iterator
-
- TripletInnerSequential() - Constructor for class etomica.atom.iterator.TripletInnerSequential
-
- tripletStart - Static variable in class etomica.virial.cluster.VirialDiagrams
-
- tripletStart - Static variable in class etomica.virial.cluster.VirialDiagramsPT
-
- trueButton() - Method in class etomica.graphics.DeviceToggleRadioButtons
-
- trueDataSource - Variable in class etomica.modules.multiharmonic.DataProcessorBias
-
- trueMultiP - Variable in class etomica.virial.cluster.VirialDiagrams
-
- trueMultiP - Variable in class etomica.virial.cluster.VirialDiagramsPT
-
- trueY - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- trunc(int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Truncate polynomial degree.
- trunc() - Method in class etomica.veos.bigdecimal.Rational
-
Remove the fractional part.
- TruncatedOctahedron - Class in etomica.math.geometry
-
A truncated octahedron is an Archimedean, space-filling polyhedron with 24
vertices, 36 edges, and 14 faces.
- TruncatedOctahedron(Space) - Constructor for class etomica.math.geometry.TruncatedOctahedron
-
Constructs a truncated octahedron with vertices defined in the embedded
space and with unit edge lengths.
- TruncatedOctahedron(Space, double) - Constructor for class etomica.math.geometry.TruncatedOctahedron
-
Constructs a truncated octahedron with vertices defined in the embedded
space and with edge lengths equal to the given value.
- truncatedPotential - Variable in class etomica.potential.Potential0Lrc
-
- truncation - Variable in class etomica.AlkaneEH.CH4NVT.Param
-
- truncation - Variable in class etomica.parser.ParserLAMMPS.Options
-
- truncation - Variable in class etomica.potential.PotentialGroupSoft
-
- truncationRadius - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- truncationRadius - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- truncationRadius - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- truncationRadius - Variable in class etomica.space.BoundaryDeformablePeriodic
-
- trycmd - Static variable in class org.jmol.script.Token
-
- TSelement - Variable in class etomica.virial.GUI.components.SimpleElementForSimilarSpecies
-
- tStep - Variable in class etomica.interfacial.LJMD.LJMDParams
-
- tStep - Variable in class etomica.liquidLJ.LjMd3D.LjMd3DParams
-
- tStep - Variable in class etomica.normalmode.SimHSMDVacancy.HSMDVParams
-
- tStepFac - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- tt0Tensor - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSC
-
- tt0Tensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- tt0Tensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- tt0Tensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- tt1Tensor - Variable in class etomica.models.co2.P2CO2Hellmann.P2CO2SC
-
- tt1Tensor - Variable in class etomica.models.water.P2WaterSzalewicz.P2H2OSC
-
- tt1Tensor - Variable in class etomica.potential.P2NitrogenHellmann.P2N2QFH
-
- tTmp - Variable in class etomica.models.co2.P2CO2H2OWheatley.P2CO2H2OSCTI
-
- tttprod - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- TTTprod(Vector, Vector, Vector, double) - Static method in class etomica.potential.P2WaterPotentialsJankowski
-
- tunable - Variable in class etomica.integrator.mcmove.MCMoveStepTracker
-
- Tungsten - Class in etomica.chem.elements
-
Class for the Tungsten element.
- Tungsten(String) - Constructor for class etomica.chem.elements.Tungsten
-
- Tungsten(String, double) - Constructor for class etomica.chem.elements.Tungsten
-
- Tunit - Variable in class etomica.models.co2.PNCO2GCPM
-
- Tunit - Variable in class etomica.models.water.PNWaterGCPM
-
- tUnit - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- tUnit - Variable in class etomica.modules.swmd.SwmdGraphic
-
- Tuple3f - Class in org.jmol.util
-
A generic 3 element tuple that is represented by single precision floating
point x,y and z coordinates.
- Tuple3f() - Constructor for class org.jmol.util.Tuple3f
-
- Tuple3i - Class in org.jmol.util
-
A 3-element tuple represented by signed integer x,y,z coordinates.
- Tuple3i() - Constructor for class org.jmol.util.Tuple3i
-
Constructs and initializes a Tuple3i to (0,0,0).
- Tuple4f - Class in org.jmol.util
-
A generic 4 element tuple that is represented by single precision floating
point x,y,z and w coordinates.
- Tuple4f() - Constructor for class org.jmol.util.Tuple4f
-
Constructs and initializes a Tuple4f to (0,0,0,0).
- tV2 - Variable in class etomica.space.BoundaryDeformablePeriodic
-
- twicesqrt3ofhalfofthebondlength - Static variable in class etomica.virial.ConformationNaphthaleneTraPPE
-
- TWO_PI - Static variable in class etomica.util.Constants
-
- tWork - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- twosqrt3a - Static variable in class etomica.virial.ConformationAnthraceneTraPPE
-
- twosqrt3a - Static variable in class etomica.virial.ConformationPhenanthreneTraPPE
-
- type - Variable in class etomica.action.activity.ControllerEvent
-
- type - Variable in class etomica.atom.Atom
-
- type - Static variable in class org.jmol.script.Token
-
- type1 - Variable in class etomica.data.meter.MeterRDF
-
- type1 - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- type2 - Variable in class etomica.data.meter.MeterRDF
-
- type2 - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- TYPE_EDGE_ANY - Static variable in interface etomica.graph.model.Metadata
-
- TYPE_NODE_DEFAULT - Static variable in interface etomica.graph.model.Metadata
-
- TYPE_NODE_FIELD - Static variable in interface etomica.graph.model.Metadata
-
- TYPE_NODE_ROOT - Static variable in interface etomica.graph.model.Metadata
-
- typeAgentManager - Variable in class etomica.integrator.IntegratorRigidIterative
-
- typeAgentManager - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- typeAgentManager - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- typeManager - Variable in class etomica.models.co2.PNGCPM
-
- typeOf(ScriptVariable) - Static method in class org.jmol.script.ScriptVariable
-
- types - Variable in class etomica.potential.Potential0Lrc
-
- types - Variable in class etomica.potential.PotentialGroup.PotentialLinker
-
- types - Variable in class etomica.potential.PotentialMaster.PotentialLinker
-
U
- u - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- u - Variable in class etomica.models.nitrogen.TestRotationVector
-
- u(double) - Method in class etomica.models.rowley.P2RepRowley
-
The energy u.
- u(double) - Method in class etomica.modules.catalysis.P2SquareWellBonding
-
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
- u(double) - Method in class etomica.modules.catalysis.P2SquareWellBondingCO
-
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
- u(double) - Method in class etomica.modules.catalysis.P2SquareWellSurface
-
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
- u(double) - Method in class etomica.modules.droplet.P2Cohesion
-
- u(double) - Method in class etomica.modules.mu.P2SquareWellOneSide
-
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
- u - Variable in class etomica.normalmode.CoordinateDefinitionLeaf
-
- u - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
-
- u - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- u - Variable in class etomica.normalmode.IntegratorHarmonic
-
- u - Variable in class etomica.normalmode.MCMoveHarmonic
-
- u - Variable in class etomica.normalmode.MCMoveHarmonicStep
-
- u(double) - Method in class etomica.normalmode.P2XOrder
-
- u(double) - Method in class etomica.potential.P1HydrogenMielke
-
- u(double) - Method in interface etomica.potential.P1IntraMolecular
-
- u(double) - Method in class etomica.potential.P2Anharmonic
-
- u(double) - Method in class etomica.potential.P2ArgonAziz1993
-
The energy u.
- u(double) - Method in class etomica.potential.P2ArgonSlavicekEtAl2003
-
The energy u.
- u(double) - Method in class etomica.potential.P2ArgonTangAndToennies2003
-
The energy u.
- u(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
-
- u(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs
-
- u(double) - Method in class etomica.potential.P2DoubleWell
-
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
- u(double) - Method in class etomica.potential.P2Dreiding
-
harmonic oscillator
- u(double) - Method in class etomica.potential.P2EffectiveFeynmanHibbs
-
- u(double) - Method in class etomica.potential.P2Electrostatic
-
- u(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
- u(double) - Method in class etomica.potential.P2Exp6
-
The energy u
- u(double) - Method in class etomica.potential.P2Exp6Buckingham
-
The energy u
- u(double) - Method in class etomica.potential.P2Fene
-
- u(double) - Method in class etomica.potential.P2HardAssociation
-
Returns -epsilon if less than well diameter, or zero otherwise.
- u(double) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- u(double) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
- u(double) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
- u(double) - Method in class etomica.potential.P2HardBond
-
Returns 0 if the bond is within the required distance, infinity if not.
- u(double) - Method in class etomica.potential.P2HardSphere
-
Interaction energy of the pair.
- u(double) - Method in class etomica.potential.P2Harmonic
-
- u(double) - Method in class etomica.potential.P2HePCKLJS.P2HeQFH
-
- u(double) - Method in class etomica.potential.P2HePCKLJS.P2HeTI
-
- u(double) - Method in class etomica.potential.P2HePCKLJS
-
The energy u.
- u(double) - Method in class etomica.potential.P2HeSimplified.P2HeQFH
-
- u(double) - Method in class etomica.potential.P2HeSimplified.P2HeTI
-
- u(double) - Method in class etomica.potential.P2HeSimplified
-
The energy u.
- u(double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
-
- u(double) - Method in class etomica.potential.P2Ideal
-
Returns zero.
- u(double) - Method in class etomica.potential.P2LennardJones
-
The energy u.
- u(double) - Method in class etomica.potential.P2LennardJonesDreiding
-
The energy u.
- u(double) - Method in class etomica.potential.P2LJQ
-
- u(double) - Method in class etomica.potential.P2LJQQ
-
- u(double) - Method in class etomica.potential.P2ModifiedMorse
-
The energy u.
- u(double) - Method in class etomica.potential.P2Morse
-
The energy u.
- u(double) - Method in class etomica.potential.P2O2Bartolomei.P2O2TI
-
- u(double) - Method in class etomica.potential.P2PenetrableBond
-
Returns 0 if the bond is within the required distance, infinity if not.
- u(double) - Method in class etomica.potential.P2PenetrableSphere
-
Returns epsilon if overlapping, or zero if not.
- u(double) - Method in class etomica.potential.P2PenetrableSquareWell
-
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
- u(double) - Method in class etomica.potential.P2QChemInterpolated
-
- u(double) - Method in class etomica.potential.P2SoftSphere
-
The energy u.
- u(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
-
- u(double) - Method in class etomica.potential.P2SoftSphericalTruncated
-
Returns the energy of the wrapped potential if the separation
is less than the cutoff value
- u(double) - Method in class etomica.potential.P2SoftSphericalTruncatedForceShifted
-
- u(double) - Method in class etomica.potential.P2SoftSphericalTruncatedShifted
-
Returns the energy of the wrapped potential if the separation
is less than the cutoff value
- u(double) - Method in class etomica.potential.P2SoftTruncated
-
- u(double) - Method in class etomica.potential.P2SquareWell
-
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
- u(double) - Method in class etomica.potential.P2SquareWellRobust
-
Returns infinity if overlapping, -epsilon if otherwise less than well diameter, or zero if neither.
- u(double) - Method in class etomica.potential.P2Tether
-
Returns infinity if separation is greater than tether distance, zero otherwise
- u(double) - Method in class etomica.potential.P2WCA
-
The energy u.
- u(double) - Method in class etomica.potential.Potential2HardSpherical
-
The pair energy u(r^2) with no truncation applied.
- u(double) - Method in interface etomica.potential.Potential2Spherical
-
The pair energy u(r^2) with no truncation applied.
- u(double) - Method in class etomica.virial.P1IntraLambda
-
- u(double) - Method in class etomica.yukawa.P2HC2Yukawa
-
Energy method.
- u(double) - Method in class etomica.yukawa.P2Yukawa
-
Energy method.
- u0 - Variable in class etomica.virial.P1IntraLambda
-
- UAlpha(double, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
-
- uBeads - Variable in class etomica.virial.PotentialGroup3PI
-
- uBeads - Variable in class etomica.virial.PotentialGroupPI
-
- UBeta(double, double) - Method in class etomica.models.nitrogen.FindTransitionTemperature
-
- uBondCorr() - Method in class etomica.potential.EwaldSummation
-
- uccageTickEdges - Static variable in class org.jmol.util.BoxInfo
-
- uCorrect - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- uCorrect - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- uCorrection(double) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
-
Long-range correction to the energy.
- uFac - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- uFcc(double, double) - Static method in class etomica.statmech.LennardJones
-
Total ensemble-averaged internal potential energy for the fcc solid.
- uFourier() - Method in class etomica.potential.EwaldSummation
-
- uFourier() - Method in class etomica.potential.EwaldSumMolecules
-
- uHarmonicNew - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- uHarmonicOld - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- uijPol - Variable in class etomica.virial.ClusterSumPolarizable
-
- uijPol - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- uijPol - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- uijPol - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- uInt(double) - Method in class etomica.models.rowley.P2RepRowley
-
Integral of the potential, used to evaluate corrections for potential truncation.
- uInt(double) - Method in class etomica.modules.droplet.P2Cohesion
-
- uInt(double) - Method in class etomica.potential.P2Anharmonic
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2ArgonAziz1993
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2ArgonSlavicekEtAl2003
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2ArgonTangAndToennies2003
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2DiscreteFeynmanHibbs.P2HeEmpericalQuantum
-
- uInt(double) - Method in class etomica.potential.P2Dreiding
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2Electrostatic
-
- uInt(double) - Method in class etomica.potential.P2ElectrostaticWithHardCore
-
- uInt(double) - Method in class etomica.potential.P2Exp6
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2Exp6Buckingham
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2Fene
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2Harmonic
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2HePCKLJS
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2HeSimplified
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2HydrogenPatkowskiIso
-
- uInt(double) - Method in class etomica.potential.P2LennardJones
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2LennardJonesDreiding
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2LJQQ
-
- uInt(double) - Method in class etomica.potential.P2ModifiedMorse
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2Morse
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2QChemInterpolated
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2SoftSphere
-
Integral used for corrections to potential truncation.
- uInt(double) - Method in class etomica.potential.P2SoftSphericalTruncated
-
Returns the value of uInt for the wrapped potential.
- uInt(double) - Method in class etomica.potential.P2WCA
-
Returns zero, since there is no long-range correction.
- uInt(double) - Method in class etomica.potential.Potential2SoftSpherical
-
Integral of the potential, used to evaluate corrections for potential truncation.
- uInt(double) - Method in class etomica.yukawa.P2HC2Yukawa
-
Integral from rC to infinity.
- uInt(double) - Method in class etomica.yukawa.P2Yukawa
-
Integral from rC to infinity.
- uIntOverQ(double, double, double) - Static method in class etomica.freeenergy.npath.SimLattice
-
- uisString(String) - Static method in class etomica.units.gui.Lister
-
- ULat - Variable in class etomica.normalmode.MeterSolidProps
-
- ULat - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- uLat0 - Static variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
Nominal function for lattice energy
- uLat0 - Static variable in class etomica.normalmode.MCMoveVolumeSolid
-
Nominal function for lattice energy
- uLat0 - Static variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
Nominal function for lattice energy
- uLat0 - Static variable in class etomica.normalmode.MeterDDP
-
Nominal function for lattice energy
- uLat0 - Static variable in class etomica.normalmode.MeterDP
-
Nominal function for lattice energy
- ulat0 - Variable in class etomica.normalmode.SoftSphereSolidEOS
-
- ulat0 - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- uLatFunction - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- uLatFunction - Variable in class etomica.normalmode.MCMoveVolumeSolid
-
- uLatFunction - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- uLatFunction - Variable in class etomica.normalmode.MeterDDP
-
- uLatFunction - Variable in class etomica.normalmode.MeterDP
-
- ulatMeasured - Variable in class etomica.normalmode.MeterBoltzmann
-
- ulatSampled - Variable in class etomica.normalmode.MeterBoltzmann
-
- uLatTruncFunction - Variable in class etomica.normalmode.MCMoveVolumeSolid
-
- ULLMAN_ALGORITHM - Static variable in interface etomica.graph.isomorphism.SearchState
-
- UllmanSearchState - Class in etomica.graph.isomorphism
-
- UllmanSearchState(Graph, Graph) - Constructor for class etomica.graph.isomorphism.UllmanSearchState
-
- UllmanSearchState(UllmanSearchState) - Constructor for class etomica.graph.isomorphism.UllmanSearchState
-
- umax - Variable in class etomica.modules.clustergenerator.Plot
-
- umin - Variable in class etomica.modules.clustergenerator.Plot
-
- una - Variable in class etomica.virial.PotentialNonAdditive
-
- Unary - Interface in etomica.graph.operations
-
- UNARY_OP_EDIF - Static variable in interface etomica.graph.engine.Parser
-
- UNARY_OP_EXP - Static variable in interface etomica.graph.engine.Parser
-
- UNARY_OP_INT - Static variable in interface etomica.graph.engine.Parser
-
- UNARY_OP_ISO - Static variable in interface etomica.graph.engine.Parser
-
- UNARY_OP_NCOPY - Static variable in interface etomica.graph.engine.Parser
-
- UNARY_OP_NDIF - Static variable in interface etomica.graph.engine.Parser
-
- UNARY_OP_PCOPY - Static variable in interface etomica.graph.engine.Parser
-
- UNARY_OP_POWER - Static variable in interface etomica.graph.engine.Parser
-
- UNARY_OP_RELABEL - Static variable in interface etomica.graph.engine.Parser
-
- UNARY_OP_SPLIT - Static variable in interface etomica.graph.engine.Parser
-
- UnaryChain - Class in etomica.graph.operations
-
Facilitates a chain of unary operations.
- UnaryChain(Unary, Unary) - Constructor for class etomica.graph.operations.UnaryChain
-
- UnaryChain.ChainParameters - Class in etomica.graph.operations
-
- UnaryOpByteImpl - Class in etomica.graph.engine.impl
-
- UnaryOpByteImpl(String, Parser.Expression, byte) - Constructor for class etomica.graph.engine.impl.UnaryOpByteImpl
-
- UnaryOpByteMapImpl - Class in etomica.graph.engine.impl
-
- UnaryOpByteMapImpl(String, Parser.Expression, Map<Byte, Byte>) - Constructor for class etomica.graph.engine.impl.UnaryOpByteMapImpl
-
- UnaryOpColorImpl - Class in etomica.graph.engine.impl
-
- UnaryOpColorImpl(String, Parser.Expression, char) - Constructor for class etomica.graph.engine.impl.UnaryOpColorImpl
-
- UnaryOpImpl - Class in etomica.graph.engine.impl
-
- UnaryOpImpl(String, Parser.Expression) - Constructor for class etomica.graph.engine.impl.UnaryOpImpl
-
- UnaryOpThreeColorImpl - Class in etomica.graph.engine.impl
-
- UnaryOpThreeColorImpl(String, Parser.Expression, char, char, char) - Constructor for class etomica.graph.engine.impl.UnaryOpThreeColorImpl
-
- UnaryOpTwoByteImpl - Class in etomica.graph.engine.impl
-
- UnaryOpTwoByteImpl(String, Parser.Expression, byte, byte) - Constructor for class etomica.graph.engine.impl.UnaryOpTwoByteImpl
-
- unbond(IAtom, IAtom) - Method in class etomica.modules.chainequilibrium.P2SquareWellBonded
-
this function unbonds two atoms
- Undefined - Class in etomica.units.dimensions
-
Undefined dimension used for quantities with undefined or unknown dimensions.
- undisplayThread - Variable in class etomica.modules.droplet.EllipseDisplayAction
-
- undo() - Method in class etomica.action.BoxInflate
-
Reverses the action of the inflation by performing the
action with a scale given the by the reciprocal of the
current scale.
- undo() - Method in class etomica.action.BoxInflateAnisotropic
-
- undo() - Method in interface etomica.action.Undoable
-
Causes the effect of most recent call to actionPerformed to be reversed.
- undo - Static variable in class org.jmol.script.Token
-
- Undoable - Interface in etomica.action
-
Interface for an action that can be "undone", such that its effect
is reversed if the undo() method is invoked immediately after the
actionPerformed().
- undomove - Static variable in class org.jmol.script.Token
-
- unescapeBitset(String) - Static method in class org.jmol.util.Escape
-
- unEscapeBitSetArray(BitSet) - Method in class org.jmol.script.ScriptVariable
-
- unEscapeBitSetArray(ArrayList<ScriptVariable>, boolean) - Static method in class org.jmol.script.ScriptVariable
-
- unescapeMatrix(String) - Static method in class org.jmol.util.Escape
-
- unescapePoint(String) - Static method in class org.jmol.util.Escape
-
- unescapePointOrBitsetAsVariable(Object) - Static method in class org.jmol.script.ScriptVariable
-
- unescapePointOrBitsetOrMatrixOrArray(String) - Static method in class org.jmol.util.Escape
-
- unescapeStringArray(String) - Static method in class org.jmol.util.Escape
-
- unescapeUnicode(String) - Static method in class org.jmol.util.Escape
-
- uNew - Variable in class etomica.association.MCMoveDimer
-
- uNew - Variable in class etomica.association.MCMoveDimerRotate
-
- uNew - Variable in class etomica.association.MCMoveSmer
-
- uNew - Variable in class etomica.association.MCMoveSmerRotate
-
- uNew - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- uNew - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- uNew - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- uNew - Variable in class etomica.integrator.mcmove.MCMoveAtom
-
- uNew - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- uNew - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- uNew - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- uNew - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- uNew - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- uNew - Variable in class etomica.models.hexane.MCMoveCBMC
-
- uNew - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- uNew - Variable in class etomica.models.hexane.MCMoveReptate
-
- uNew - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- uNew - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- uNew - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- uNew - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- uNew - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- uNew - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- uNew - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- uNew - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- uNew - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- uNew - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- uNew - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- uNew - Variable in class etomica.spin.MCMoveSpinFlip
-
- uNew - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- uNew - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- uNew - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- uNew - Variable in class etomica.virial.MCMoveClusterRingScale
-
- uNewPE - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- Unfactor - Class in etomica.graph.operations
-
This operation will do the reverse of the Factor operation.
- Unfactor() - Constructor for class etomica.graph.operations.Unfactor
-
- Union - Class in etomica.graph.operations
-
- Union() - Constructor for class etomica.graph.operations.Union
-
- unit - Variable in class etomica.graphics.Device
-
- unit - Variable in class etomica.graphics.DisplayTextBox
-
Physical units associated with the displayed value.
- UNIT - Static variable in class etomica.units.Ampere
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Angstrom
-
Singleton instance of this unit
- UNIT - Static variable in class etomica.units.Bar
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Barye
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.BohrRadius
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Calorie
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Candela
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Coulomb
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Count
-
Singleton instance of this unit
- UNIT - Static variable in class etomica.units.CubicCentimeter
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.CubicMeter
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Dalton
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Debye
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Decimal
-
Singleton instance of this unit
- UNIT - Static variable in class etomica.units.Degree
-
Single instance of this unit.
- UNIT - Static variable in class etomica.units.dimensions.Null
-
Unit for an otherwise unspecified dimensionless quantity.
- UNIT - Static variable in class etomica.units.dimensions.Undefined
-
Unit for a quantity having undefined or unknown units.
- UNIT - Static variable in class etomica.units.Dyne
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Electron
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.ElectronVolt
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Erg
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Gram
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Hartree
-
Hartree unit of energy, corresponding to the approximate energy of
hydrogen in its ground state.
- UNIT - Static variable in class etomica.units.Hertz
-
Singleton instance of this class.
- UNIT - Static variable in class etomica.units.Joule
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Kelvin
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Liter
-
Singleton instance of this class.
- UNIT - Static variable in class etomica.units.Meter
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Mole
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Newton
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Pascal
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Percent
-
Singleton instance of this unit
- UNIT - Static variable in class etomica.units.Picosecond
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Poise
-
Singleton instance of this unit.
- unit() - Method in class etomica.units.PrefixedUnit
-
- UNIT - Static variable in class etomica.units.Radian
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Second
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Statcoulomb
-
Convenience instance of this unit to permit unit to be assigned
without creating a new instance of it each time
- Unit - Interface in etomica.units
-
Interface used to specify the physical units to be used when inputting or
outputting a quantity.
- UNIT - Static variable in class etomica.units.Volt
-
Singleton instance of this unit.
- UNIT - Static variable in class etomica.units.Watt
-
Singleton instance of this unit.
- unit() - Method in enum etomica.virial.GUI.models.EnumPotentialParamDescription
-
- unitAxisVectors - Static variable in class org.jmol.viewer.JmolConstants
-
- unitCell() - Method in class etomica.lattice.crystal.Primitive
-
Returns a the unit cell specified by this primitive.
- unitCell() - Method in class etomica.lattice.crystal.PrimitiveCubic
-
Returns a new Square (if primitive is 2D) or Cube (if 3D) with edges
given by the size of the primitive vectors.
- unitCell() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
Returns a new Cuboid with edges of length given by the current
values of the primitive vectors.
- unitCell() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
Returns a new Cuboid with edges of length given by the current
values of the primitive vectors.
- unitCell() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
Returns a new Cuboid with edges given by the lengths of the
primitive vectors.
- unitcell - Static variable in class org.jmol.script.Token
-
- unitcellcolor - Static variable in class org.jmol.script.Token
-
- unitCubePoints - Static variable in class org.jmol.util.BoxInfo
-
- UnitFilter - Class in etomica.units.gui
-
- UnitFilter() - Constructor for class etomica.units.gui.UnitFilter
-
- UnitGraphics - Class in etomica.units.gui
-
- UnitGraphics() - Constructor for class etomica.units.gui.UnitGraphics
-
- unitList - Variable in class etomica.graphics.DisplayPlot
-
- UnitRatio - Class in etomica.units
-
Class for constructing units forms as ratios of other units.
- UnitRatio(Unit, Unit) - Constructor for class etomica.units.UnitRatio
-
Constructs the compound unit using conversion factors and labels from the
constituent units.
- UnitRatio(Unit, Unit, String, String) - Constructor for class etomica.units.UnitRatio
-
- units - Variable in class etomica.graphics.DisplayTable
-
- unitSelector() - Method in class etomica.graphics.DimensionedDoubleEditor
-
Returns a combo box that can be used to select the unit.
- unitString() - Static method in class etomica.units.gui.Lister
-
- UnitSystem - Class in etomica.units.systems
-
Specifies a system of units.
- UnitSystem() - Constructor for class etomica.units.systems.UnitSystem
-
- UnitSystem.Sim - Class in etomica.units.systems
-
System of units based on simulation units of Daltons, picoseconds, and Angstroms
- unitSystemString() - Static method in class etomica.units.gui.Lister
-
- unitx - Static variable in class org.jmol.script.Token
-
- unitxyz - Static variable in class org.jmol.script.Token
-
- unity - Static variable in class org.jmol.script.Token
-
- unitz - Static variable in class org.jmol.script.Token
-
- UNMASK_CHANGEABLE_TRANSLUCENT - Static variable in class org.jmol.util.Colix
-
- unPause() - Method in class etomica.action.activity.ActivityGroupParallel
-
- unPause() - Method in class etomica.action.activity.ActivityGroupSeries
-
Removes activity group from the paused state, resuming execution where it
left off.
- unPause() - Method in class etomica.action.Activity
-
Removes activity from the paused state, resuming execution where it left
off.
- unsafe() - Method in class etomica.modules.colloid.ColloidSim.CriterionNone
-
- unsafe() - Method in class etomica.modules.render.RenderMD.CriterionCar
-
- unsafe() - Method in class etomica.modules.sam.CriterionTether3
-
- unsafe() - Method in class etomica.nbr.CriterionAdapter
-
Indicates whether the atom has changed (e.g.
- unsafe() - Method in class etomica.nbr.CriterionAll
-
Always returns false, indicating that neighbor list never needs updating.
- unsafe() - Method in class etomica.nbr.CriterionNone
-
Always returns false, indicating that neighbor list never needs updating.
- unsafe() - Method in class etomica.nbr.CriterionPositionWall
-
- unsafe() - Method in class etomica.nbr.CriterionSimple
-
- unsafe() - Method in class etomica.nbr.molecule.CriterionAdapterMolecular
-
Indicates whether the atom has changed (e.g.
- unsafe() - Method in class etomica.nbr.molecule.CriterionAllMolecular
-
Always returns false, indicating that neighbor list never needs updating.
- unsafe() - Method in class etomica.nbr.molecule.CriterionSimpleMolecular
-
- unsafe() - Method in interface etomica.nbr.molecule.NeighborCriterionMolecular
-
Indicates whether the molecule has changed (e.g.
- unsafe() - Method in interface etomica.nbr.NeighborCriterion
-
Indicates whether the atom has changed (e.g.
- unscaleAtoms(double) - Method in class etomica.association.MCMoveVolumeAssociated
-
- unscaleAtoms(double) - Method in class etomica.association.MCMoveVolumeAssociatedMolecule
-
- unscreenedCount - Variable in class etomica.virial.MeterVirialBDBin
-
- unscreenedCount - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- unscreenedCount - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- unscreenedCount - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- unseenNeighbor(byte, byte) - Method in class etomica.graph.traversal.AbstractTraversal
-
- unset() - Method in class etomica.atom.iterator.ANIntergroupCoupled
-
- unset() - Method in class etomica.atom.iterator.ANIntergroupExchange
-
- unset() - Method in class etomica.atom.iterator.ANIntragroupExchange
-
- unset() - Method in class etomica.atom.iterator.ApiIndexList
-
Sets iterator to a state where hasNext() returns false.
- unset() - Method in class etomica.atom.iterator.ApiInnerVariable
-
Sets the iterator such that hasNext is false.
- unset() - Method in class etomica.atom.iterator.ApiInterArrayList
-
Sets iterator such that hasNext is false.
- unset() - Method in class etomica.atom.iterator.ApiIntergroup
-
Sets the iterator such that hasNext is false.
- unset() - Method in class etomica.atom.iterator.ApiIntraArrayList
-
Sets iterator such that next is null.
- unset() - Method in class etomica.atom.iterator.ApiIntragroup
-
- unset() - Method in class etomica.atom.iterator.AtomIteratorAllLeafType
-
- unset() - Method in class etomica.atom.iterator.AtomIteratorArrayList
-
- unset() - Method in class etomica.atom.iterator.AtomIteratorArrayListAdjacent
-
Puts iterator in a state where hasNext is false.
- unset() - Method in class etomica.atom.iterator.AtomIteratorArrayListSimple
-
Puts iterator in state in which hasNext is false.
- unset() - Method in class etomica.atom.iterator.AtomIteratorNull
-
- unset() - Method in class etomica.atom.iterator.AtomIteratorSinglet
-
Sets iterator to a state where hasNext() returns false.
- unset() - Method in class etomica.atom.iterator.Atomset3IteratorIndexList
-
Sets iterator to a state where hasNext() returns false.
- unset() - Method in class etomica.atom.iterator.Atomset4IteratorIndexList
-
Sets iterator to a state where hasNext() returns false.
- unset() - Method in interface etomica.atom.iterator.AtomsetIterator
-
Puts iterator in a state in which hasNext() returns false.
- unset() - Method in class etomica.atom.iterator.AtomsetIteratorAllLeafAtoms
-
- unset() - Method in class etomica.atom.iterator.TripletInnerSequential
-
- unset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorBruteForce
-
- unset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbr
-
- unset() - Method in class etomica.integrator.mcmove.MCMoveInsertDeleteLatticeVacancy.AtomIteratorNbrCell
-
- unset() - Method in class etomica.lattice.RectangularLattice.Iterator
-
- unset() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
Puts iterator in a state in which hasNext() returns false.
- unset() - Method in interface etomica.lattice.SiteIterator
-
Puts the iterator in a state such that hasNext is false.
- unset() - Method in class etomica.molecule.iterator.MoleculeIteratorAll
-
- unset() - Method in class etomica.molecule.iterator.MoleculeIteratorArrayList
-
- unset() - Method in class etomica.molecule.iterator.MoleculeIteratorArrayListSimple
-
Puts iterator in state in which hasNext is false.
- unset() - Method in class etomica.molecule.iterator.MoleculeIteratorSinglet
-
Sets iterator to a state where hasNext() returns false.
- unset() - Method in class etomica.molecule.iterator.MpiInnerFixed
-
Sets the iterator such that hasNext is false.
- unset() - Method in class etomica.molecule.iterator.MpiInnerVariable
-
Sets the iterator such that hasNext is false.
- unset() - Method in class etomica.molecule.iterator.MpiInterArrayList
-
Sets iterator such that hasNext is false.
- unset() - Method in class etomica.molecule.iterator.MpiInterspecies1A
-
- unset() - Method in class etomica.molecule.iterator.MpiInterspeciesAA
-
Sets iterator such that hasNext is false.
- unset() - Method in class etomica.molecule.iterator.MpiIntraArrayList
-
Sets iterator such that next is null.
- unset() - Method in class etomica.molecule.iterator.MpiIntraspecies1A
-
- unset() - Method in class etomica.molecule.iterator.MpiIntraspeciesAA
-
Sets iterator such that next is null.
- unset() - Method in class etomica.molecule.iterator.MpiMolecule
-
Sets iterator to state in which hasNext is false.
- unset() - Method in class etomica.nbr.cell.Api1ACell
-
- unset() - Method in class etomica.nbr.cell.ApiAACell
-
- unset() - Method in class etomica.nbr.cell.AtomIteratorCell
-
- unset() - Method in class etomica.nbr.cell.molecule.MoleculeIteratorCell
-
- unset() - Method in class etomica.nbr.cell.molecule.Mpi1ACell
-
- unset() - Method in class etomica.nbr.cell.molecule.MpiAACell
-
- unset() - Method in class etomica.nbr.site.Api1ASite
-
- unset() - Method in class etomica.potential.PotentialMaster.AtomIterator0
-
- unset() - Method in class etomica.potential.PotentialMaster.MoleculeIterator0
-
- untransform(double[], double[], IFunction) - Method in class etomica.data.AccumulatorAverageBootstrap
-
- uOld - Variable in class etomica.association.MCMoveDimer
-
- uOld - Variable in class etomica.association.MCMoveDimerRotate
-
- uOld - Variable in class etomica.association.MCMoveSmer
-
- uOld - Variable in class etomica.association.MCMoveSmerRotate
-
- uOld - Variable in class etomica.freeenergy.npath.MCMoveAtomCoupled
-
- uOld - Variable in class etomica.freeenergy.npath.MCMoveAtomSwap
-
- uOld - Variable in class etomica.gaussianwork.MCMoveMultiHarmonic
-
- uOld - Variable in class etomica.integrator.mcmove.MCMoveAtom
-
- uOld - Variable in class etomica.integrator.mcmove.MCMoveDimer
-
- uOld - Variable in class etomica.integrator.mcmove.MCMoveDimerRotate
-
- uOld - Variable in class etomica.integrator.mcmove.MCMoveInsertDelete
-
- uOld - Variable in class etomica.integrator.mcmove.MCMoveMolecule
-
- uOld - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- uOld - Variable in class etomica.models.hexane.MCMoveCBMC
-
- uOld - Variable in class etomica.models.hexane.MCMoveCombinedCbmcTranslation
-
- uOld - Variable in class etomica.models.hexane.MCMoveReptate
-
- uOld - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledInitPert
-
- uOld - Variable in class etomica.models.nitrogen.MCMoveMoleculeCoupledSuperBox
-
- uOld - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleModes
-
- uOld - Variable in class etomica.models.oneDHardRods.MCMoveChangeMultipleWV
-
- uOld - Variable in class etomica.models.oneDHardRods.MCMoveCompareMultipleWV
-
- uOld - Variable in class etomica.modules.multiharmonic.MCMoveMultiHarmonic
-
- uOld - Variable in class etomica.normalmode.IntegratorHarmonic
-
- uOld - Variable in class etomica.normalmode.MCMoveAtomCoupled
-
- uOld - Variable in class etomica.normalmode.MCMoveAtomCoupledBennet
-
- uOld - Variable in class etomica.normalmode.MCMoveAtomCoupledUmbrella
-
- uOld - Variable in class etomica.normalmode.MCMoveAtomSuperBox
-
- uOld - Variable in class etomica.normalmode.MCMoveHarmonic
-
- uOld - Variable in class etomica.normalmode.MCMoveHarmonicStep
-
- uOld - Variable in class etomica.normalmode.MCMoveMoleculeCoupled
-
- uOld - Variable in class etomica.normalmode.MCMoveSingleMode
-
- uOld - Variable in class etomica.normalmode.MCMoveVolumeMonoclinicScaled
-
- uOld - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- uOld - Variable in class etomica.paracetamol.MCMoveMoleculeCoupledDLPOLY
-
- uOld - Variable in class etomica.spin.MCMoveSpinFlip
-
- uOld - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- uOld - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- uOld - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- uOld - Variable in class etomica.virial.MCMoveClusterRingScale
-
- uOldPE - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DSuperBox
-
- uPair - Variable in class etomica.virial.PotentialCommonAtomic
-
- update() - Method in class etomica.data.DataSourceFunction
-
Updates the wrapped Data and DataInfo for change to the xDataSource
- update(double[][], DataDoubleArray.DataInfoDoubleArray[]) - Method in class etomica.data.DataSourceIndependentSimple
-
- update(double[], DataDoubleArray.DataInfoDoubleArray) - Method in class etomica.data.DataSourceIndependentSimple
-
- update(double[], double[]) - Method in class etomica.data.DataSourcePoints
-
- update(Set<Graph>) - Method in interface etomica.graph.engine.Viewer
-
- update(Set<Graph>) - Method in class etomica.graph.viewer.ClusterViewer
-
- update() - Method in class etomica.lattice.crystal.Primitive
-
- update() - Method in class etomica.lattice.crystal.PrimitiveBcc
-
- update() - Method in class etomica.lattice.crystal.PrimitiveCubic
-
- update() - Method in class etomica.lattice.crystal.PrimitiveFcc
-
- update() - Method in class etomica.lattice.crystal.PrimitiveGeneral
-
- update() - Method in class etomica.lattice.crystal.PrimitiveHexagonal.PrimitiveHexagonalReciprocal
-
- update() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- update() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D.PrimitiveHexagonal2DReciprocal
-
- update() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- update() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic.PrimitiveMonoclinicReciprocal
-
- update() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- update() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- update() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
- update() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- update() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- update() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- update() - Method in class etomica.models.hexane.PrimitiveHexane
-
- update(Graphics) - Method in class etomica.modules.clustergenerator.Plot
-
- update() - Method in class etomica.modules.crystalviewer.ClipPlaneEditor
-
- update(BravaisLattice) - Method in class etomica.modules.crystalviewer.CrystalViewer
-
- update() - Method in class etomica.modules.crystalviewer.LatticeEditor
-
- update() - Method in class etomica.modules.sam.SamGraphic.ModifierWallPosition
-
- update() - Method in class etomica.space.BoundaryDeformablePeriodic
-
- update(Graphics) - Method in class etomica.util.Grabber.ImagePanel
-
- updateAtom(IAtom) - Method in class etomica.integrator.IntegratorHard
-
updates collision time for a single atom (and any atom that might a
collision with the atom)
- updateAtom(IAtom) - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
-
- updateAtoms(AtomPair) - Method in class etomica.integrator.IntegratorHard
-
Updates collision times/partners for collider and partner, and
for atoms that were to collide with one of them.
- updateBegin() - Method in interface etomica.graph.engine.Console
-
- updateBegin() - Method in class etomica.graph.engine.ConsoleUI
-
- updateConformation(int) - Method in class etomica.modules.sam.Sam
-
- updateCounts(boolean, double) - Method in class etomica.integrator.mcmove.MCMoveStepTracker
-
- updateCounts(boolean, double) - Method in class etomica.integrator.mcmove.MCMoveTracker
-
Updates statistics regarding the acceptance rate of this move.
- updateDataMap() - Method in class etomica.data.DataSet
-
This updates the mapping between pseudo DataSinks and indices (used for
getData(int), etc.).
- updateDimensions() - Method in class etomica.space.BoundaryRectangular
-
- updateDimensions() - Method in class etomica.space.BoundaryRectangularPeriodic
-
- updateDimensions() - Method in class etomica.space.BoundaryRectangularPore
-
- updateDimensions() - Method in class etomica.space.BoundaryRectangularSlit
-
- updateDone() - Method in interface etomica.graph.engine.Console
-
- updateDone() - Method in class etomica.graph.engine.ConsoleUI
-
- updateDrawType() - Method in class g3dsys.images.ImageShell
-
Updates line-drawing status depending on whether images are
on and the current draw boundary type.
- updateEditor() - Method in class etomica.graphics.PropertyText
-
- updateF() - Method in class etomica.data.DataSourceFunction
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterChainHS
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterChainSoft
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterSinglyConnected
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterSum
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterSumEF
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterSumHS
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterSumMultibody
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterSumMultibodyShell
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterSumShell
-
- updateF(CoordinatePairSet, AtomPairSet) - Method in class etomica.virial.ClusterTree
-
- updateF(CoordinatePairLeafSet, AtomPairSet) - Method in class etomica.virial.ClusterTreeEF
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS.AllSigs
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- updateF() - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoft
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBD
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBDMix
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- updateF(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftMix
-
- updateFlowLines() - Method in class etomica.modules.rheology.RheologyGraphic
-
- updateIntegrator() - Method in class etomica.graphics.DeviceThermoSelector
-
set the integrator's temperature to the selected value
- updateLine(int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- updateLists() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
- updateLists() - Method in class etomica.nbr.list.NeighborListManager
-
- updateMrLast() - Method in class etomica.integrator.IntegratorVerlet
-
- updateNbrsIfNeeded() - Method in class etomica.nbr.list.molecule.NeighborListManagerMolecular
-
Checks whether any atom needs neighbor list updating, and if
one is found, performs neighbor list updates of all atom
neighbor lists.
- updateNbrsIfNeeded() - Method in class etomica.nbr.list.NeighborListManager
-
Checks whether any atom needs neighbor list updating, and if
one is found, performs neighbor list updates of all atom
neighbor lists.
- updateNeighborList() - Method in class etomica.lattice.RectangularLatticeNbrIterator
-
- updateNeighborList() - Method in class etomica.lattice.RectangularLatticeNbrIteratorAdjacent
-
- updateNeighborList() - Method in class etomica.lattice.RectangularLatticeNbrIteratorSquare
-
Method called on reset if any calls were previously made
to setLattice, setSite, setRange, or setDirection.
- updateNewMoleculePair(int[]) - Method in class etomica.models.nitrogen.FindPairMoleculeIndex
-
- updateNewMoleculePair(int[]) - Method in class etomica.models.nitrogen.FindPairMoleculeIndexBetaN2
-
- updatePiston() - Method in class etomica.modules.pistoncylinder.IntegratorHardPiston
-
recalculate collision times for all atoms with the wall/piston
- updatePlane(int) - Method in class etomica.graphics.DisplayBoxCanvasG3DSys
-
- updateProperty(String, PropertyUpdate) - Method in class etomica.server.resources.PropertiesResource
-
- updateQuaternion() - Method in class etomica.math.Quaternion
-
First checks if all the components are numbers.
- updateRCut() - Method in class etomica.modules.sam.Sam
-
- updateVertices() - Method in class etomica.math.geometry.Cube
-
- updateVertices() - Method in class etomica.math.geometry.Cuboid
-
- updateVertices() - Method in class etomica.math.geometry.LineSegment
-
- updateVertices() - Method in class etomica.math.geometry.Parallelepiped
-
Calculated vertices based on current values of edge vectors.
- updateVertices() - Method in class etomica.math.geometry.Parallelogram
-
Calculated vertices based on current values of edge vectors.
- updateVertices() - Method in class etomica.math.geometry.Point
-
Does nothing; the point is the vertex.
- updateVertices() - Method in class etomica.math.geometry.PolygonGeneral
-
- updateVertices() - Method in class etomica.math.geometry.PolyhedronGeneral
-
Calculates vertices from their internal representation, which
for a general polyhedron does nothing because the vertices are
the internal representation.
- updateVertices() - Method in class etomica.math.geometry.Polytope
-
This method should be defined by the subclass to calculate the vertices
in accordance with the internal representation of the polytope.
- updateVertices() - Method in class etomica.math.geometry.Rectangle
-
- updateVertices() - Method in class etomica.math.geometry.Square
-
- updateVertices() - Method in class etomica.math.geometry.TruncatedOctahedron
-
The following defines the vertices that the truncated octahedron will
have, based on Vector3D.
- upList - Variable in class etomica.integrator.IntegratorHard
-
- upList - Variable in class etomica.nbr.list.AtomNeighborLists
-
- upList - Variable in class etomica.nbr.list.molecule.MoleculeNeighborLists
-
- upListNow - Variable in class etomica.atom.iterator.AtomIteratorArrayList
-
- upListNow - Variable in class etomica.molecule.iterator.MoleculeIteratorArrayList
-
- upListNow - Variable in class etomica.molecule.iterator.MpiIntraspecies1A
-
- UpolAtkins - Variable in class etomica.models.co2.PNCO2GCPM
-
- UPPER_MASK - Static variable in class etomica.util.random.RandomMersenneTwister
-
- uR - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- uReactCO - Variable in class etomica.modules.catalysis.ReactionManagerCO
-
- uReactCORev - Variable in class etomica.modules.catalysis.ReactionManagerCO
-
- uReal() - Method in class etomica.potential.EwaldSummation
-
- uReal() - Method in class etomica.potential.EwaldSumMolecules
-
- USAGE - Static variable in class etomica.graph.view.rasterizer.Main
-
Describes the command line options for the rasterizer
- usage() - Static method in class etomica.math.numerical.AkimaSplineSmootherMain
-
- uSCFData - Variable in class etomica.potential.P2QChemInterpolated
-
- USE_PALETTE - Static variable in class org.jmol.util.Colix
-
- usearcball - Static variable in class org.jmol.script.Token
-
- useC10 - Static variable in class etomica.potential.P2HeSimplified
-
- useE - Variable in class etomica.virial.PYGenerator.IteratorEF
-
- uSelf() - Method in class etomica.potential.EwaldSummation
-
- uSelf() - Method in class etomica.potential.EwaldSumMolecules
-
- useminimizationthread - Static variable in class org.jmol.script.Token
-
- useNeighborLists - Variable in class etomica.simulation.prototypes.HSMD3D.HSMD3DParam
-
Flag indicating whether neighbor list is to be used, default = true
- usenumberlocalization - Static variable in class org.jmol.script.Token
-
- usePermutations - Variable in class etomica.virial.ClusterBonds
-
- usePhongExponent - Static variable in class org.jmol.util.Shader
-
- usercolorscheme - Static variable in class org.jmol.script.Token
-
- useReverseEdges - Static variable in class etomica.graph.model.impl.GraphImpl
-
- userStylesheet - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
User stylesheet
- useSurfaceOnly - Variable in class etomica.modules.droplet.P2Cohesion
-
- useSZ - Variable in class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
-
- useUB - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- useUB - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- Ushcats - Class in etomica.veos
-
- Ushcats(BetaSource, int) - Constructor for class etomica.veos.Ushcats
-
- UShift(P2SoftSphericalTruncated) - Constructor for class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
-
- uShift - Variable in class etomica.normalmode.SimLJVacancy
-
- uShift - Variable in class etomica.rotation.P2LJDipole
-
- USine(P2SoftSphericalTruncated, double[][], double) - Constructor for class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
-
- uSplitter - Variable in class etomica.normalmode.DataSourceMuRoot
-
- uStaticFcc(double) - Static method in class etomica.statmech.LennardJones
-
Potential energy per atom of a static fcc lattice with a LJ particle at
each site.
- uSums - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
- uTriplet - Variable in class etomica.virial.PotentialCommonAtomic
-
- uValues - Variable in class etomica.virial.MCMoveClusterPolyhedraChain
-
- uValues - Variable in class etomica.virial.MCMoveClusterPolyhedraTree
-
V
- V - Variable in class etomica.dimer.IntegratorDimerRT
-
- v(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
-
- v(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
-
- v(double, double) - Method in interface etomica.mappedvirial.PotentialCalculationMappedVirialV.VFunc
-
- v - Variable in class etomica.modules.droplet.DropletAtomicGraphic.DataSourceVaporDensity
-
- v - Variable in class etomica.nbr.cell.molecule.NeighborCellManagerMolecular
-
- v - Variable in class etomica.nbr.cell.NeighborCellManager
-
- v - Variable in class etomica.normalmode.HSNPT.ActionSummer
-
- v - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- v - Variable in class etomica.paracetamol.AnalyticalDerivativeEnergyParacetamol
-
- v - Variable in class etomica.potential.P2SpheroPolyhedron
-
- v - Variable in class etomica.potential.P3HydrogenManzhos.P3HydrogenManzhosMolecular
-
- v - Variable in class etomica.virial.IntSet
-
- v0 - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- v0 - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- v1 - Variable in class etomica.config.ConformationChainZigZag
-
- v1 - Variable in class etomica.config.ConformationChainZigZag2
-
- v1 - Variable in class etomica.potential.P4BondTorsion
-
- v1 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- v2 - Variable in class etomica.config.ConformationChainZigZag
-
- v2 - Variable in class etomica.config.ConformationChainZigZag2
-
- v2 - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- v2 - Variable in class etomica.normalmode.HSNPT.ColorSchemeDisplacement
-
- v2 - Variable in class etomica.potential.P4BondTorsion
-
- v2 - Variable in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- v2 - Variable in class etomica.space3d.OrientationFull3D
-
- v3 - Variable in class etomica.space3d.OrientationFull3D
-
- valence - Static variable in class org.jmol.script.Token
-
- validate - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Validation flag
- validateBondList(IAtom, IAtomList, boolean) - Method in class etomica.association.AssociationHelperBranched
-
Returns false if invalid bonding is recognized
- validateBondList(IAtom, IAtomList, boolean) - Method in class etomica.association.AssociationHelperDouble
-
- validateBondList(IMolecule, IMoleculeList, boolean) - Method in class etomica.association.AssociationHelperMolecule
-
Returns false if invalid bonding is recognized
- validateConverterConfig(SVGConverter) - Method in class etomica.graph.view.rasterizer.Main
-
Template methods which subclasses may implement to do whatever is
needed.
- value - Variable in class etomica.compatibility.NumericFeature
-
- value - Variable in class etomica.compatibility.StringFeature
-
- value(Graph) - Static method in class etomica.graph.property.NumFieldNodes
-
- value(Graph) - Static method in class etomica.graph.property.NumRootNodes
-
- value - Variable in class etomica.graphics.DisplayTextBox
-
Object for displaying the value as a text field
- value() - Method in enum etomica.units.Prefix
-
- value() - Method in class etomica.veos.BigValue
-
Returns the value held by the instance (in true form, not as log, and with sign applied).
- value() - Method in interface etomica.veos.IBigValue
-
Returns the value held by the instance (in true form, not as log, and with sign applied).
- value() - Method in class etomica.veos.MyBigDecimal
-
Returns the value held by the instance (in true form, not as log, and with sign applied).
- value(double) - Static method in class etomica.virial.B3LJ
-
- value(List, boolean) - Method in class etomica.virial.CalcFFT
-
- value(double[][]) - Method in class etomica.virial.cluster.ClusterCollapsedTreeNode
-
- value(double[][]) - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- value(double[][]) - Method in class etomica.virial.cluster.ClusterTreeNode
-
- value(BoxCluster) - Method in interface etomica.virial.ClusterAbstract
-
Value of this cluster for the given pairset at the specified reciprocal
temperature.
- value(double[][][]) - Method in class etomica.virial.ClusterBonds
-
Returns the value of the cluster for the given set of atom pairs at the
given value of beta = 1/kT.
- value(double[][][], double[][]) - Method in class etomica.virial.ClusterBondsNonAdditive
-
- value - Variable in class etomica.virial.ClusterChainHS
-
- value(BoxCluster) - Method in class etomica.virial.ClusterChainHS
-
- value - Variable in class etomica.virial.ClusterChainSoft
-
- value(BoxCluster) - Method in class etomica.virial.ClusterChainSoft
-
- value - Variable in class etomica.virial.ClusterCoupledFlipped
-
- value(BoxCluster) - Method in class etomica.virial.ClusterCoupledFlipped
-
- value - Variable in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- value(BoxCluster) - Method in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- value - Variable in class etomica.virial.ClusterCoupledFlippedPartial
-
- value(BoxCluster) - Method in class etomica.virial.ClusterCoupledFlippedPartial
-
- value(BoxCluster) - Method in class etomica.virial.ClusterDifference
-
- value(BoxCluster) - Method in class etomica.virial.ClusterExchange
-
- value(BoxCluster) - Method in class etomica.virial.ClusterMultiToSingle
-
- value - Variable in class etomica.virial.ClusterSinglyConnected
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSinglyConnected
-
- value - Variable in class etomica.virial.ClusterSum
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSum
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSumExternalField
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSumHS
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSumIC
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSumMultibody
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSumNonAdditiveTrimerEnergy
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizable
-
- value - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct
-
- value - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4Pt
-
- value - Variable in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSumPolarizableWertheimProduct4PtFinal
-
- value(BoxCluster) - Method in class etomica.virial.ClusterSumStickyEF
-
- value(BoxCluster) - Method in class etomica.virial.ClusterTree
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWeightAbs
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWeightSumWall
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWeightUmbrella
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- value - Variable in class etomica.virial.ClusterWheatleyHS
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWheatleyHS
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivatives.ClusterRetrievePrimes
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWheatleyMultibodyDerivativesBD.ClusterRetrievePrimes
-
- value - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWheatleyPartitionScreening
-
- value - Variable in class etomica.virial.ClusterWheatleySoft
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoft
-
- value - Variable in class etomica.virial.ClusterWheatleySoftBD
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftBD
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivatives.ClusterRetrievePrimes
-
- value - Variable in class etomica.virial.ClusterWheatleySoftDerivatives
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivatives
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD.ClusterRetrievePrimes
-
- value - Variable in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- value(BoxCluster) - Method in class etomica.virial.ClusterWheatleySoftDerivativesBD
-
- value() - Method in interface etomica.virial.IntSet.PropertyBin
-
- value(BoxCluster) - Method in class etomica.virial.simulations.VirialH2OGCPMD.Clusterfoo
-
- value(int, int[]) - Method in class etomica.virial.simulations.VirialHSBinMultiThreaded.DooDad
-
- value - Variable in class org.jmol.script.Token
-
- value12(int) - Method in class etomica.virial.ClusterSumIC
-
- valueArray(BoxCluster) - Method in class etomica.virial.ClusterWheatleyExtendSW
-
- ValueCache(DataSourceScalar, Integrator) - Constructor for class etomica.liquidLJ.LjMd3D.ValueCache
-
- ValueCache - Class in etomica.liquidLJ
-
- ValueCache(DataSourceScalar, Integrator) - Constructor for class etomica.liquidLJ.ValueCache
-
- valueChanged(ListSelectionEvent) - Method in class etomica.veos.bigdecimal.Wigner3jGUI
-
Interpreter parser loop.
- valueClusters - Variable in class etomica.virial.simulations.SimulationVirialOverlap2
-
- valueEditor() - Method in class etomica.graphics.DimensionedDoubleEditor
-
- valueForSig(long) - Method in class etomica.virial.ClusterWheatleyHS.AllSigs
-
- ValueImpl - Class in etomica.graph.engine.impl
-
- ValueImpl(String) - Constructor for class etomica.graph.engine.impl.ValueImpl
-
- valueOf(String) - Static method in enum etomica.action.activity.Controller.ActionStatus
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.action.activity.ControllerEvent.Type
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.data.DataSourceUniform.LimitType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.graphics.DeviceBox.LabelType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.graphics.DisplayTextBox.LabelType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.integrator.IntegratorMD.ThermostatType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.models.co2.P2CO2Hellmann.Parameters
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.models.co2.PNCO2GCPM.Component
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.models.co2.PNGCPM.Component
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.models.water.P2WaterSzalewicz.Component
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.models.water.PNWaterGCPM.Component
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.parser.ParserLAMMPS.Truncation
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.potential.IteratorDirective.Direction
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.server.representations.StatusAction.Status
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.units.Prefix
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.util.Constants.CompassDirection
-
Returns the enum constant of this type with the specified name.
- valueOf(Vector<BigInteger>, BigInteger) - Static method in class etomica.veos.bigdecimal.BigIntegerMath
-
Evaluate the value of an integer polynomial at some integer argument.
- valueOf(BigInteger) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Evaluate at some integer argument.
- valueOf(int) - Method in class etomica.veos.bigdecimal.BigIntegerPoly
-
Horner scheme to find the function value at the argument x
- valueOf(String) - Static method in enum etomica.virial.GUI.models.EnumPotentialParamDescription
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.virial.GUI.models.EnumSiteName
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.virial.simulations.VirialHePI.FlexApproach
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.virial.simulations.VirialHSOrC.PotentialChoice
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum etomica.virial.simulations.VirialLJOrC.PotentialChoice
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumPalette
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumStereoMode
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.jmol.constant.EnumVdw
-
Returns the enum constant of this type with the specified name.
- valueProps - Variable in class etomica.meta.wrappers.Wrapper
-
- values() - Static method in enum etomica.action.activity.Controller.ActionStatus
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.action.activity.ControllerEvent.Type
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.data.DataSourceUniform.LimitType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.graphics.DeviceBox.LabelType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.graphics.DisplayTextBox.LabelType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.integrator.IntegratorMD.ThermostatType
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.models.co2.P2CO2Hellmann.Parameters
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.models.co2.PNCO2GCPM.Component
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.models.co2.PNGCPM.Component
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.models.water.P2WaterSzalewicz.Component
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.models.water.PNWaterGCPM.Component
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.parser.ParserLAMMPS.Truncation
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.potential.IteratorDirective.Direction
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values - Static variable in class etomica.potential.P2WaterPotentialsJankowski
-
- values() - Static method in enum etomica.server.representations.StatusAction.Status
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.units.Prefix
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Method in class etomica.util.collections.IndexMap
-
- values() - Static method in enum etomica.util.Constants.CompassDirection
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.virial.GUI.models.EnumPotentialParamDescription
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.virial.GUI.models.EnumSiteName
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.virial.simulations.VirialHePI.FlexApproach
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.virial.simulations.VirialHSOrC.PotentialChoice
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum etomica.virial.simulations.VirialLJOrC.PotentialChoice
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.constant.EnumPalette
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.constant.EnumStereoMode
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- values() - Static method in enum org.jmol.constant.EnumVdw
-
Returns an array containing the constants of this enum type, in
the order they are declared.
- valueUsingPermutations(double[][][]) - Method in class etomica.virial.ClusterBonds
-
Returns value obtained by averaging over all unique permutations of the
point indices.
- VanderWaals - Class in etomica.veos
-
- VanderWaals(double) - Constructor for class etomica.veos.VanderWaals
-
- VanderWaals(double, int) - Constructor for class etomica.veos.VanderWaals
-
- vanderwaals - Static variable in class org.jmol.script.Token
-
- vanderwaalsMars - Static variable in class org.jmol.util.Elements
-
Default table of van der Waals Radii.
- vaporColor - Variable in class etomica.modules.droplet.ColorSchemeLiquidVapor
-
- vaporFccCoexDensities(double) - Static method in class etomica.statmech.LennardJones
-
Returns the densities of coexisting (saturated) vapor and fcc phases
(sublimation densities).
- vaporFccCoexPressure(double) - Static method in class etomica.statmech.LennardJones
-
Returns the saturation pressure for vapor-fcc coexistence.
- VariableImpl - Class in etomica.graph.engine.impl
-
- VariableImpl(String) - Constructor for class etomica.graph.engine.impl.VariableImpl
-
- vBias - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- vBias - Variable in class etomica.liquidLJ.LjMd3D.DataProcessorReweight
-
- vBias - Variable in class etomica.liquidLJ.MeterWidomInsertionCorrection
-
- vCO - Variable in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
-
- vCO - Variable in class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- vCount - Variable in class etomica.virial.ClusterWheatleyPartitionScreening
-
- vCut - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- vCut - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- vCut - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- vCut - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- vCut2 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
-
- vCut2 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
-
- vDataSource - Variable in class etomica.data.meter.MeterPressureByVolumeChange
-
- VdwPROBE - Static variable in class org.jmol.util.Elements
-
- vec - Variable in class etomica.math.Quaternion
-
- vec - Variable in class etomica.potential.P3HydrogenManzhos
-
- vector - Variable in class etomica.data.DataSourceAtomDistance
-
- vector - Variable in class etomica.models.nitrogen.ConformationNitrogen
-
- vector - Variable in class etomica.models.nitrogen.ConformationNitrogenShellModel
-
- Vector - Interface in etomica.space
-
Interface containing vector operations, accessor, and mutator methods.
- vector - Variable in class etomica.virial.Conformation7SiteRigidSF6
-
- vector - Variable in class etomica.virial.ConformationAnthracene3site
-
- vector - Variable in class etomica.virial.ConformationAnthraceneTraPPE
-
- vector - Variable in class etomica.virial.ConformationCO2
-
- vector - Variable in class etomica.virial.ConformationNaphthaleneTraPPE
-
- vector - Variable in class etomica.virial.ConformationPh3site
-
- vector - Variable in class etomica.virial.ConformationPhenanthreneTraPPE
-
- vector - Static variable in class org.jmol.script.Token
-
- vector1 - Variable in class etomica.virial.MCMoveClusterMoleculeLayerMove
-
- Vector1D - Class in etomica.space1d
-
Implementation of the Vector class for a 1-dimensional space.
- Vector1D() - Constructor for class etomica.space1d.Vector1D
-
- Vector1D(double) - Constructor for class etomica.space1d.Vector1D
-
- Vector1D(double[]) - Constructor for class etomica.space1d.Vector1D
-
- Vector1D(Vector1D) - Constructor for class etomica.space1d.Vector1D
-
- vector2 - Variable in class etomica.virial.MCMoveClusterMoleculeLayerMove
-
- Vector2D - Class in etomica.space2d
-
Implementation of the Vector class for a 2-dimensional space.
- Vector2D() - Constructor for class etomica.space2d.Vector2D
-
- Vector2D(double, double) - Constructor for class etomica.space2d.Vector2D
-
- Vector2D(double[]) - Constructor for class etomica.space2d.Vector2D
-
- Vector2D(Vector2D) - Constructor for class etomica.space2d.Vector2D
-
- Vector3D - Class in etomica.space3d
-
Implementation of the Vector class for a 3-dimensional space.
- Vector3D() - Constructor for class etomica.space3d.Vector3D
-
- Vector3D(double, double, double) - Constructor for class etomica.space3d.Vector3D
-
- Vector3D(double[]) - Constructor for class etomica.space3d.Vector3D
-
- Vector3D(Vector3D) - Constructor for class etomica.space3d.Vector3D
-
- Vector3f - Class in org.jmol.util
-
A 3-element vector that is represented by single precision floating point
x,y,z coordinates.
- Vector3f() - Constructor for class org.jmol.util.Vector3f
-
- VectorForce(Space) - Constructor for class etomica.normalmode.LJVacancyMin.VectorForce
-
- VectorND - Class in etomica.spaceNd
-
Implementation of the Vector class for a 3-dimensional space.
- VectorND(int) - Constructor for class etomica.spaceNd.VectorND
-
- VectorND(double[]) - Constructor for class etomica.spaceNd.VectorND
-
- VectorProperty - Class in etomica.meta.properties
-
Created by kofke on 7/24/17.
- VectorProperty(Object, PropertyDescriptor) - Constructor for class etomica.meta.properties.VectorProperty
-
- vectorR - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- vectors - Variable in class etomica.config.ConformationChain2D
-
- vectors() - Method in class etomica.lattice.crystal.Primitive
-
Returns the primitive vectors.
- vectors - Variable in class org.jmol.util.Quadric
-
- vectorscale - Static variable in class org.jmol.script.Token
-
- VectorSerializer - Class in etomica.meta.serializers
-
- VectorSerializer() - Constructor for class etomica.meta.serializers.VectorSerializer
-
- VectorSource(Space) - Constructor for class etomica.integrator.IntegratorMD.VectorSource
-
- vectorsymmetry - Static variable in class org.jmol.script.Token
-
- vEHS - Variable in class etomica.virial.simulations.ShapeParser.ShapeData
-
- velocity - Variable in class etomica.atom.AtomLeafDynamic
-
- velocity - Variable in class etomica.molecule.MoleculeOrientedDynamic
-
- Velocity - Class in etomica.units.dimensions
-
Dimension for all units of velocity, Length/Time
- velocityButton - Variable in class etomica.modules.pistoncylinder.PistonCylinderGraphic
-
- VEOS3SW - Class in etomica.modules.adsorption
-
- VEOS3SW() - Constructor for class etomica.modules.adsorption.VEOS3SW
-
- verbose - Variable in class etomica.math.numerical.NewtonMinimization
-
- verbose - Variable in class etomica.normalmode.LJVacancyMin.SimOverlapParam
-
- verbose - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- verbose - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- verbose - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- verbose - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- verbose - Variable in class etomica.virial.BnPYCHe.BnPYHeParams
-
- Verlet() - Method in class etomica.threads.ThreadsMD
-
- version - Static variable in class org.jmol.viewer.JmolConstants
-
- vertexColixes - Variable in class org.jmol.util.MeshSurface
-
- vertexCount - Variable in class org.jmol.util.MeshSurface
-
- vertexCount0 - Variable in class org.jmol.util.MeshSurface
-
- vertexSets - Variable in class org.jmol.util.MeshSurface
-
- vertexSource - Variable in class org.jmol.util.MeshSurface
-
- vertexValues - Variable in class org.jmol.util.MeshSurface
-
- vertices - Variable in class etomica.atom.AtomTypeSpheroPolyhedron
-
- vertices - Variable in class etomica.math.geometry.Polytope
-
These vertices are used in all external representations of the polygon.
- vertices - Variable in class etomica.virial.simulations.ShapeParser.ShapeData
-
- vertices - Variable in class org.jmol.util.MeshSurface
-
- vf - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- VF2_ALGORITHM - Static variable in interface etomica.graph.isomorphism.SearchState
-
- VF2SearchState - Class in etomica.graph.isomorphism
-
- VF2SearchState(Graph, Graph) - Constructor for class etomica.graph.isomorphism.VF2SearchState
-
- VF2SearchState(VF2SearchState) - Constructor for class etomica.graph.isomorphism.VF2SearchState
-
- VF_ALGORITHM - Static variable in interface etomica.graph.isomorphism.SearchState
-
- VFSearchState - Class in etomica.graph.isomorphism
-
- VFSearchState(Graph, Graph) - Constructor for class etomica.graph.isomorphism.VFSearchState
-
- VFSearchState(VFSearchState) - Constructor for class etomica.graph.isomorphism.VFSearchState
-
- vH2H2(double, double, double, double, double, double) - Method in class etomica.potential.P2HydrogenHinde
-
- vH2H2(double, double, double, double, double, double) - Method in class etomica.potential.P2HydrogenHindeAtomic
-
- vH2H2(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowski
-
- vH2H2(double, double, double, double) - Method in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- vH2H2H2(Vector[]) - Method in class etomica.potential.P3HydrogenManzhos
-
- vhs - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- vhs - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- vib - Variable in class etomica.dimer.IntegratorDimerMin
-
- vib - Variable in class etomica.dimer.IntegratorDimerRT
-
- vib0 - Variable in class etomica.normalmode.SoftSphereSolidEOS
-
- vib0 - Variable in class etomica.normalmode.SoftSphereSolidEOSCalculator
-
- vibration - Static variable in class org.jmol.script.Token
-
- vibrationperiod - Static variable in class org.jmol.script.Token
-
- vibrationscale - Static variable in class org.jmol.script.Token
-
- vibx - Static variable in class org.jmol.script.Token
-
- vibxyz - Static variable in class org.jmol.script.Token
-
- viby - Static variable in class org.jmol.script.Token
-
- vibz - Static variable in class org.jmol.script.Token
-
- ViewAlertMsgBox - Class in etomica.virial.GUI.views
-
- ViewAlertMsgBox(String) - Constructor for class etomica.virial.GUI.views.ViewAlertMsgBox
-
- ViewAlertMsgBoxSpeciesRemoval - Class in etomica.virial.GUI.views
-
- ViewAlertMsgBoxSpeciesRemoval(String) - Constructor for class etomica.virial.GUI.views.ViewAlertMsgBoxSpeciesRemoval
-
- ViewAlkaneLengthSelection - Class in etomica.virial.GUI.views
-
- ViewAlkaneLengthSelection(String) - Constructor for class etomica.virial.GUI.views.ViewAlkaneLengthSelection
-
- ViewConsoleOutputBox - Class in etomica.virial.GUI.views
-
- ViewConsoleOutputBox() - Constructor for class etomica.virial.GUI.views.ViewConsoleOutputBox
-
- Viewer - Interface in etomica.graph.engine
-
- viewer - Variable in class etomica.modules.crystalviewer.LatticeEditor
-
- ViewSimEnvironmentSelection - Class in etomica.virial.GUI.views
-
- ViewSimEnvironmentSelection(ModelSimulationEnvironment) - Constructor for class etomica.virial.GUI.views.ViewSimEnvironmentSelection
-
- ViewSpeciesSelection - Class in etomica.virial.GUI.models
-
- ViewSpeciesSelection(ModelSpeciesSelection, ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.models.ViewSpeciesSelection
-
- ViewSpeciesSelection - Class in etomica.virial.GUI.views
-
- ViewSpeciesSelection(ModelSpeciesSelection, ModelSelectedSpecies) - Constructor for class etomica.virial.GUI.views.ViewSpeciesSelection
-
- virial(IAtomList) - Method in class etomica.dimer.P1LepsHarmonic
-
- virial(IAtomList) - Method in class etomica.freeenergy.npath.P1ImageHarmonic
-
- virial(IAtomList) - Method in class etomica.interfacial.P1Wall
-
- virial - Variable in class etomica.liquidLJ.MeterPU
-
- virial(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMulti
-
Virial of the pair as given by the du(double) method
- virial(IAtomList) - Method in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat
-
Virial of the pair as given by the du(double) method
- virial(IAtomList) - Method in class etomica.meam.P2EAM
-
- virial(IAtomList) - Method in class etomica.meam.PotentialCuLREP
-
- virial(IAtomList) - Method in class etomica.meam.PotentialEAM
-
- virial(IAtomList) - Method in class etomica.meam.PotentialEAM_LS
-
- virial(IAtomList) - Method in class etomica.meam.PotentialEFS
-
- virial(IAtomList) - Method in class etomica.meam.PotentialMEAM
-
- virial(IAtomList) - Method in class etomica.models.co2.P2CO2H2OWheatley
-
- virial(IAtomList) - Method in class etomica.models.co2.P2CO2Hellmann
-
- virial(IMoleculeList) - Method in class etomica.models.nitrogen.P2Nitrogen
-
- virial(IMoleculeList) - Method in class etomica.models.nitrogen.P2NitrogenAB
-
- virial(IMoleculeList) - Method in class etomica.models.nitrogen.P2NitrogenShellModel
-
- virial(IMoleculeList) - Method in class etomica.models.water.P2Water3PSoft
-
- virial(IMoleculeList) - Method in class etomica.models.water.P2Water4PSoft
-
- virial(IAtomList) - Method in class etomica.models.water.P2WaterSzalewicz
-
- virial(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAPorousWall
-
- virial(IAtomList) - Method in class etomica.modules.dcvgcmd.P1WCAWall
-
- virial(IAtomList) - Method in class etomica.modules.droplet.P1Smash
-
- virial(IAtomList) - Method in class etomica.modules.droplet.P2Cohesion
-
- virial(IAtomList) - Method in class etomica.modules.materialfracture.P1Tension
-
- virial(IAtomList) - Method in class etomica.modules.rosmosis.P1Tether
-
- virial(IAtomList) - Method in class etomica.modules.sam.P1Sinusoidal
-
- virial(IAtomList) - Method in class etomica.modules.sam.P1WCAWall
-
- virial(IAtomList) - Method in class etomica.potential.EwaldSummation.P2EwaldReal
-
- virial(IAtomList) - Method in class etomica.potential.EwaldSummation
-
- virial(IAtomList) - Method in class etomica.potential.P1Harmonic
-
- virial(IAtomList) - Method in class etomica.potential.P1HarmonicSite
-
- virial(IAtomList) - Method in class etomica.potential.P1SoftBoundary
-
- virial(IAtomList) - Method in class etomica.potential.P2HardAssociationConeDoubleSites
-
- virial(IAtomList) - Method in class etomica.potential.P2HardAssociationConeFourSites
-
- virial(IAtomList) - Method in class etomica.potential.P2HardAssociationConeOneSite
-
- virial(IMoleculeList) - Method in class etomica.potential.P2HSDipole
-
- virial(IAtomList) - Method in class etomica.potential.P2Ideal
-
Returns zero.
- virial(IMoleculeList) - Method in class etomica.potential.P2LJDipole
-
- virial(IAtomList) - Method in class etomica.potential.P2LJQ
-
- virial(IMoleculeList) - Method in class etomica.potential.P2MoleculeSoftTruncatedSwitched
-
- virial(IAtomList) - Method in class etomica.potential.P2NitrogenHellmann
-
- virial(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipole
-
- virial(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated.P0ReactionField
-
- virial(IMoleculeList) - Method in class etomica.potential.P2ReactionFieldDipoleTruncated
-
- virial(IAtomList) - Method in class etomica.potential.P2SoftSphericalTruncated.P0Lrc
-
- virial(IAtomList) - Method in class etomica.potential.P2SoftSphericalTruncatedSwitched
-
- virial(IAtomList) - Method in class etomica.potential.P2SoftTruncated
-
Returns the 2nd derivative (r^2 d^2u/dr^2) of the wrapped potential if the separation
is less than the cutoff value
- virial(IAtomList) - Method in class etomica.potential.P3BondAngle
-
- virial(IAtomList) - Method in class etomica.potential.P3BondAngleDreiding
-
- virial(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHe
-
- virial(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- virial(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- virial(IAtomList) - Method in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- virial(IAtomList) - Method in class etomica.potential.P4BondTorsion
-
- virial(IAtomList) - Method in class etomica.potential.P4BondTorsionAlkaneXCCH
-
- virial(IAtomList) - Method in class etomica.potential.P4BondTorsionOPLS
-
- virial(IAtomList) - Method in class etomica.potential.P4TorsionDreiding
-
- virial(IAtomList) - Method in class etomica.potential.Potential2SoftSpherical
-
Virial of the pair as given by the du(double) method
- virial(IAtomList) - Method in class etomica.potential.Potential2SoftSphericalLS
-
Virial of the pair as given by the du(double) method
- virial(IMoleculeList) - Method in class etomica.potential.PotentialGroupSoft
-
- virial(IMoleculeList) - Method in interface etomica.potential.PotentialMolecularSoft
-
- virial(IAtomList) - Method in interface etomica.potential.PotentialSoft
-
- virial(IMoleculeList) - Method in class etomica.rotation.P2LJDipole
-
- Virial2CLJQ - Class in etomica.virial.simulations
-
LJ simulation using Mayer sampling to evaluate cluster integrals
- Virial2CLJQ() - Constructor for class etomica.virial.simulations.Virial2CLJQ
-
- Virial2CLJQ.Virial2CLJQParam - Class in etomica.virial.simulations
-
Inner class for parameters
- Virial2CLJQParam() - Constructor for class etomica.virial.simulations.Virial2CLJQ.Virial2CLJQParam
-
- Virial7SiteRigidSF6 - Class in etomica.virial.simulations
-
Virial coefficients calculation of SF6
7 sites LJ + rigid without Coulombic interaction
Reference: Samios, Molecular force field investigation for sulfur hexafluoride: A computer simulation study
Mayer sampling to evaluate cluster integrals
- Virial7SiteRigidSF6() - Constructor for class etomica.virial.simulations.Virial7SiteRigidSF6
-
- Virial7SiteRigidSF6.VirialSF6Param - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAceticAcid - Class in etomica.virial.simulations
-
Mayer-sampling MC simulation for acetic acid using IMPROVED OPLS united-atom model
- VirialAceticAcid() - Constructor for class etomica.virial.simulations.VirialAceticAcid
-
- VirialAceticAcid.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAceticAcidFlex - Class in etomica.virial.simulations
-
Mayer-sampling MC simulation for acetic acid using IMPROVED TraPPE-UA model
Flexible correction is included
- VirialAceticAcidFlex() - Constructor for class etomica.virial.simulations.VirialAceticAcidFlex
-
- VirialAceticAcidFlex.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAlkane - Class in etomica.virial.simulations
-
Mayer sampling simulation for alkanes using the TraPPE force field.
- VirialAlkane() - Constructor for class etomica.virial.simulations.VirialAlkane
-
- VirialAlkane.VirialSiepmannSpheresParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAlkaneEHTest - Class in etomica.virial.simulations
-
Mayer sampling simulation for alkanes using the TraPPE-Explicit Hydrogen force field.
- VirialAlkaneEHTest() - Constructor for class etomica.virial.simulations.VirialAlkaneEHTest
-
- VirialAlkaneEHTest.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAlkaneFlex - Class in etomica.virial.simulations
-
Mayer sampling simulation for alkanes using the TraPPE force field.
- VirialAlkaneFlex() - Constructor for class etomica.virial.simulations.VirialAlkaneFlex
-
- VirialAlkaneFlex.VirialSiepmannSpheresParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAlkaneFull - Class in etomica.virial.simulations
-
Mayer sampling simulation for alkanes using the TraPPE-United Atoms force field.
- VirialAlkaneFull() - Constructor for class etomica.virial.simulations.VirialAlkaneFull
-
- VirialAlkaneFull.VirialSiepmannSpheresParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAlkaneMix - Class in etomica.virial.simulations
-
Mayer sampling simulation for alkanes using the dispersion interaction.
- VirialAlkaneMix() - Constructor for class etomica.virial.simulations.VirialAlkaneMix
-
- VirialAlkaneMix.VirialAlkaneMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAlkaneMix2 - Class in etomica.virial.simulations
-
- VirialAlkaneMix2() - Constructor for class etomica.virial.simulations.VirialAlkaneMix2
-
- VirialAlkaneMix2.VirialAlkaneMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAlkaneMix2_Kong - Class in etomica.virial.simulations
-
- VirialAlkaneMix2_Kong() - Constructor for class etomica.virial.simulations.VirialAlkaneMix2_Kong
-
- VirialAlkaneMix2_Kong.VirialAlkaneMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAlkaneMix_Kong - Class in etomica.virial.simulations
-
- VirialAlkaneMix_Kong() - Constructor for class etomica.virial.simulations.VirialAlkaneMix_Kong
-
- VirialAlkaneMix_Kong.VirialAlkaneMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAlkaneMixParam() - Constructor for class etomica.virial.simulations.VirialAlkaneMix.VirialAlkaneMixParam
-
- VirialAlkaneMixParam() - Constructor for class etomica.virial.simulations.VirialAlkaneMix2.VirialAlkaneMixParam
-
- VirialAlkaneMixParam() - Constructor for class etomica.virial.simulations.VirialAlkaneMix2_Kong.VirialAlkaneMixParam
-
- VirialAlkaneMixParam() - Constructor for class etomica.virial.simulations.VirialAlkaneMix_Kong.VirialAlkaneMixParam
-
- VirialAlkaneSKS - Class in etomica.virial.simulations
-
Mayer sampling simulation for alkanes using the SKS force field.
- VirialAlkaneSKS() - Constructor for class etomica.virial.simulations.VirialAlkaneSKS
-
- VirialAlkaneSKS.VirialSiepmannSpheresParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialAnthracene464 - Class in etomica.virial.simulations
-
Anthracene model , pure
support for CO2/An mixture calculation
3 site model from Iwai, this is 464 model
Mayer sampling to evaluate cluster integrals
- VirialAnthracene464() - Constructor for class etomica.virial.simulations.VirialAnthracene464
-
- VirialAnthracene464.VirialAnthracene545Param - Class in etomica.virial.simulations
-
6
Inner class for parameters
- VirialAnthracene545 - Class in etomica.virial.simulations
-
Anthracene model , pure
support for CO2/An mixture calculation
3 site model from Iwai this is 545 model
Mayer sampling to evaluate cluster integrals
- VirialAnthracene545() - Constructor for class etomica.virial.simulations.VirialAnthracene545
-
- VirialAnthracene545.VirialAnthracene545Param - Class in etomica.virial.simulations
-
6
Inner class for parameters
- VirialAnthracene545Param() - Constructor for class etomica.virial.simulations.VirialAnthracene464.VirialAnthracene545Param
-
- VirialAnthracene545Param() - Constructor for class etomica.virial.simulations.VirialAnthracene545.VirialAnthracene545Param
-
- VirialAnthraceneTraPPE - Class in etomica.virial.simulations
-
calculate the virial coefficients of Anthracene at given temperature
united atom TraPPE model, LJ no electrostatic, reference: TraPPE , Siepmann
* Mayer sampling to evaluate cluster integrals
- VirialAnthraceneTraPPE() - Constructor for class etomica.virial.simulations.VirialAnthraceneTraPPE
-
- VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam - Class in etomica.virial.simulations
-
6
Inner class for parameters
- VirialAnthraceneTraPPEParam() - Constructor for class etomica.virial.simulations.VirialAnthraceneTraPPE.VirialAnthraceneTraPPEParam
-
- VirialAssociatingFluid - Class in etomica.virial.simulations
-
- VirialAssociatingFluid() - Constructor for class etomica.virial.simulations.VirialAssociatingFluid
-
- VirialAssociatingFluid.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- VirialAssociatingFluid4points - Class in etomica.virial.simulations
-
- VirialAssociatingFluid4points() - Constructor for class etomica.virial.simulations.VirialAssociatingFluid4points
-
- VirialAssociatingFluid4points.VirialAssociatingFluidParam - Class in etomica.virial.simulations
-
- VirialAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid2.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid4Points.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.VirialAssociatingFluid.VirialAssociatingFluidParam
-
- VirialAssociatingFluidParam() - Constructor for class etomica.virial.simulations.VirialAssociatingFluid4points.VirialAssociatingFluidParam
-
- VirialB2WaterTIP4P_DHS_difference - Class in etomica.virial.simulations
-
for water TIP4P
B2, dielectric constant
exp (-beta u(water) ) - exp(-beta u(DHS) )
- VirialB2WaterTIP4P_DHS_difference() - Constructor for class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference
-
- VirialB2WaterTIP4P_DHS_difference.MuDeltaEBond - Class in etomica.virial.simulations
-
- VirialB2WaterTIP4P_DHS_difference.P2WaterDHS - Class in etomica.virial.simulations
-
- VirialB2WaterTIP4P_DHS_difference.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialB3C1HSDipole - Class in etomica.virial.simulations
-
B3,C1, dielectric constant
hard sphere with dipole in the center
three f bonds with mu_i * mu_j
June 2014
- VirialB3C1HSDipole() - Constructor for class etomica.virial.simulations.VirialB3C1HSDipole
-
- VirialB3C1HSDipole.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialB3C1TIP4Pwater - Class in etomica.virial.simulations
-
B3, C1, dielectric virial coefficient, TIP4P water
three f bonds with mu_i * mu_j
Dec 2014
- VirialB3C1TIP4Pwater() - Constructor for class etomica.virial.simulations.VirialB3C1TIP4Pwater
-
- VirialB3C1TIP4Pwater.MuFBond - Class in etomica.virial.simulations
-
- VirialB3C1TIP4Pwater.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialB3C2HSDipole - Class in etomica.virial.simulations
-
B3,C2, dielectric constant
part two, test
hard sphere with dipole in the center
June 2014
- VirialB3C2HSDipole() - Constructor for class etomica.virial.simulations.VirialB3C2HSDipole
-
- VirialB3C2HSDipole.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialB3C2TIP4Pwater - Class in etomica.virial.simulations
-
B3,C2, dielectric virial coefficient, TIP4P water
two f bonds, one bond of mu_i * mu_j
Dec 2014
- VirialB3C2TIP4Pwater() - Constructor for class etomica.virial.simulations.VirialB3C2TIP4Pwater
-
- VirialB3C2TIP4Pwater.fPlusBetaEU - Class in etomica.virial.simulations
-
- VirialB3C2TIP4Pwater.MuProduct - Class in etomica.virial.simulations
-
- VirialB3C2TIP4Pwater.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCH4AlkaneEHMix - Class in etomica.virial.simulations
-
Mayer sampling simulation for CH4(rigid, TraPPE-EH)-alkanes(TraPPE-EH) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=1])
- VirialCH4AlkaneEHMix() - Constructor for class etomica.virial.simulations.VirialCH4AlkaneEHMix
-
- VirialCH4AlkaneEHMix.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- virialCluster(int, MayerFunction, MayerFunction, byte) - Static method in class etomica.virial.cluster.ClusterAssociation
-
- virialCluster(int, MayerFunction, boolean, MayerFunction, boolean) - Static method in class etomica.virial.cluster.Standard
-
- virialClusterMixture(int, MayerFunction[][], MayerFunction[][], int[]) - Static method in class etomica.virial.cluster.Standard
-
- virialClusterPolarizable(int, MayerFunction, boolean, boolean) - Static method in class etomica.virial.cluster.Standard
-
- virialClusterXS(int, MayerFunction, boolean, MayerFunction, boolean, int) - Static method in class etomica.virial.cluster.Standard
-
- VirialCO2 - Class in etomica.virial.simulations
-
LJ simulation using Mayer sampling to evaluate cluster integrals
- VirialCO2() - Constructor for class etomica.virial.simulations.VirialCO2
-
- VirialCO2.VirialCO2Param - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2AlkaneEHMix - Class in etomica.virial.simulations
-
Mayer sampling simulation for CO2(rigid, TraPPE)-alkanes(TraPPE-EH) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams and flex diagrams are calculated separately (Bij = Bij[flexID=-1] + Bij[flexID=1])
- VirialCO2AlkaneEHMix() - Constructor for class etomica.virial.simulations.VirialCO2AlkaneEHMix
-
- VirialCO2AlkaneEHMix.VirialMixParam - Class in etomica.virial.simulations
-
- VirialCO2AlkaneUAMix - Class in etomica.virial.simulations
-
Mayer sampling simulation for CO2(rigid, TraPPE)-alkanes(TraPPE-UA) mixture cross virial coefficients
eovererr can be used
Using VirialDiagramMix2 to generate diagrams
see "VirialCO2AlkaneUARigid" B11 code(use rigid mix diagram)
rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=0])
- VirialCO2AlkaneUAMix() - Constructor for class etomica.virial.simulations.VirialCO2AlkaneUAMix
-
- VirialCO2AlkaneUAMix.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2anthracene464 - Class in etomica.virial.simulations
-
virial coefficients calculation
mixture of CO2 and anthracene
the code is modified from VirialCO2anthrancene545
Mayer sampling to evaluate cluster integrals
CO2 is modeled as single site, anthracene is model as three site model (464)
this is from Iwai et al, Monte carlo simulation of solubilities of Na, PH and An supercritical, Fluid Phase Equilibria 1998
- VirialCO2anthracene464() - Constructor for class etomica.virial.simulations.VirialCO2anthracene464
-
- VirialCO2anthracene464.VirialCO2anthracene545Param - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2anthracene545 - Class in etomica.virial.simulations
-
virial coefficients calculation
mixture of CO2 and anthracene
the code is modified from virialco2SKSmix
Mayer sampling to evaluate cluster integrals
CO2 is modeled as single site, anthracene is model as three site model
this is from Iwai et al, Monte carlo simulation of solubilities of Na, PH and An supercritical, Fluid Phase Equilibria 1998
they modeled using 464 model or 545 model, this is 545 model
- VirialCO2anthracene545() - Constructor for class etomica.virial.simulations.VirialCO2anthracene545
-
- VirialCO2anthracene545.VirialCO2anthracene545Param - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2anthracene545Param() - Constructor for class etomica.virial.simulations.VirialCO2anthracene464.VirialCO2anthracene545Param
-
- VirialCO2anthracene545Param() - Constructor for class etomica.virial.simulations.VirialCO2anthracene545.VirialCO2anthracene545Param
-
- VirialCO2AnthraceneTraPPE - Class in etomica.virial.simulations
-
TraPPE
mixture of CO2 and Anthracene
the code is modified from CO2/naphthalene TraPPE
LJ simulation using Mayer sampling to evaluate cluster integrals
- VirialCO2AnthraceneTraPPE() - Constructor for class etomica.virial.simulations.VirialCO2AnthraceneTraPPE
-
- VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2AnthraceneTraPPEParam() - Constructor for class etomica.virial.simulations.VirialCO2AnthraceneTraPPE.VirialCO2AnthraceneTraPPEParam
-
- VirialCO2CH4Mix - Class in etomica.virial.simulations
-
Mayer sampling simulation for CO2(rigid, TraPPE)-CH4(rigid, TraPPE-EH) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams only since both of the components are rigid
- VirialCO2CH4Mix() - Constructor for class etomica.virial.simulations.VirialCO2CH4Mix
-
- VirialCO2CH4Mix.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2CH4UAMix - Class in etomica.virial.simulations
-
Mayer sampling simulation for CO2(rigid, TraPPE)-CH4(rigid, TraPPE-UA, single LJ site) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
both of the components are rigid
- VirialCO2CH4UAMix() - Constructor for class etomica.virial.simulations.VirialCO2CH4UAMix
-
- VirialCO2CH4UAMix.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2CH4UAMixWheatley - Class in etomica.virial.simulations
-
Mayer sampling simulation for CO2(rigid, TraPPE)-CH4(rigid, TraPPE-UA, single LJ site) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
both of the components are rigid
Implement Wheatley method
- VirialCO2CH4UAMixWheatley() - Constructor for class etomica.virial.simulations.VirialCO2CH4UAMixWheatley
-
- VirialCO2CH4UAMixWheatley.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2H2OGCPM - Class in etomica.virial.simulations
-
Computes CO2-H2O mixture virial coefficients using ab-initio potentials
for both components.
- VirialCO2H2OGCPM() - Constructor for class etomica.virial.simulations.VirialCO2H2OGCPM
-
- VirialCO2H2OGCPM.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2H2OGCPMX - Class in etomica.virial.simulations
-
Computes CO2-H2O mixture virial coefficients using ab-initio potentials
for both components.
- VirialCO2H2OGCPMX() - Constructor for class etomica.virial.simulations.VirialCO2H2OGCPMX
-
- VirialCO2H2OGCPMX.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2H2OSC - Class in etomica.virial.simulations
-
Computes CO2-H2O mixture virial coefficients using ab-initio potentials
for both components.
- VirialCO2H2OSC() - Constructor for class etomica.virial.simulations.VirialCO2H2OSC
-
- VirialCO2H2OSC.VirialCO2SCParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2LJQ - Class in etomica.virial.simulations
-
single site LJ +QQ CO2 model , pure
Mayer sampling to evaluate cluster integrals with overlap sampling
From Albo model
- VirialCO2LJQ() - Constructor for class etomica.virial.simulations.VirialCO2LJQ
-
- VirialCO2LJQ.VirialCO2LJQParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2LJQParam() - Constructor for class etomica.virial.simulations.VirialCO2LJQ.VirialCO2LJQParam
-
- VirialCO2N2Mix - Class in etomica.virial.simulations
-
Mayer sampling simulation for CO2(rigid, TraPPE)-N2(rigid, TraPPE) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams only since both of the components are rigid
- VirialCO2N2Mix() - Constructor for class etomica.virial.simulations.VirialCO2N2Mix
-
- VirialCO2N2Mix.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2NaphthaleneLJQ - Class in etomica.virial.simulations
-
single site for CO2 and single site for naphthalene
mixture of CO2 and Naphthalene
the code is modified from virialco2SKSmix and virialCO2NaphthaleneTraPPE
LJ simulation using Mayer sampling to evaluate cluster integrals
parameters are from albo et al
- VirialCO2NaphthaleneLJQ() - Constructor for class etomica.virial.simulations.VirialCO2NaphthaleneLJQ
-
- VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2NaphthaleneLJQParam() - Constructor for class etomica.virial.simulations.VirialCO2NaphthaleneLJQ.VirialCO2NaphthaleneLJQParam
-
- VirialCO2NaphthaleneTraPPE - Class in etomica.virial.simulations
-
TraPPE
mixture of CO2 and Naphthalene
the code is modified from virialco2SKSmix
LJ simulation using Mayer sampling to evaluate cluster integrals
- VirialCO2NaphthaleneTraPPE() - Constructor for class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE
-
- VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2Param() - Constructor for class etomica.virial.simulations.VirialCO2.VirialCO2Param
-
- VirialCO2Param() - Constructor for class etomica.virial.simulations.VirialCO2SKSMix.VirialCO2Param
-
- VirialCO2PI - Class in etomica.virial.simulations
-
Mayer sampling simulation for path-integral virial coefficients of CO2.
- VirialCO2PI() - Constructor for class etomica.virial.simulations.VirialCO2PI
-
- VirialCO2PI.VirialH2PIParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2SCParam() - Constructor for class etomica.virial.simulations.VirialCO2H2OSC.VirialCO2SCParam
-
- VirialCO2SKSMix - Class in etomica.virial.simulations
-
LJ simulation using Mayer sampling to evaluate cluster integrals
- VirialCO2SKSMix() - Constructor for class etomica.virial.simulations.VirialCO2SKSMix
-
- VirialCO2SKSMix.VirialCO2Param - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2TraPPE - Class in etomica.virial.simulations
-
TraPPE CO2 model , pure
LJ + electrostatic
Mayer sampling to evaluate cluster integrals
- VirialCO2TraPPE() - Constructor for class etomica.virial.simulations.VirialCO2TraPPE
-
- VirialCO2TraPPE.VirialCO2TraPPEParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCO2TraPPEParam() - Constructor for class etomica.virial.simulations.VirialCO2NaphthaleneTraPPE.VirialCO2TraPPEParam
-
- VirialCO2TraPPEParam() - Constructor for class etomica.virial.simulations.VirialCO2TraPPE.VirialCO2TraPPEParam
-
- VirialCPSHeliumNonAdditive - Class in etomica.virial.simulations
-
- VirialCPSHeliumNonAdditive() - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditive
-
- VirialCPSHeliumNonAdditive.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCPSHeliumNonAdditiveClassical - Class in etomica.virial.simulations
-
- VirialCPSHeliumNonAdditiveClassical(Space) - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical
-
- VirialCPSHeliumNonAdditiveClassical.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialCPSHeliumNonAdditiveClassical_Correction - Class in etomica.virial.simulations
-
- VirialCPSHeliumNonAdditiveClassical_Correction(Space) - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction
-
- VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- virialData - Variable in class etomica.modules.interfacial.DataProcessorInterfacialTensionProfile
-
- VirialDiagrams - Class in etomica.virial.cluster
-
- VirialDiagrams(int, boolean, boolean) - Constructor for class etomica.virial.cluster.VirialDiagrams
-
- VirialDiagrams(int, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.VirialDiagrams
-
- VirialDiagrams.ArticulatedAt0 - Class in etomica.virial.cluster
-
- VirialDiagrams.ComparatorNumFieldNodesExchange - Class in etomica.virial.cluster
-
- VirialDiagramsMix - Class in etomica.virial.cluster
-
- VirialDiagramsMix(int, boolean[], boolean[]) - Constructor for class etomica.virial.cluster.VirialDiagramsMix
-
- VirialDiagramsMix(int, boolean[], boolean[], boolean) - Constructor for class etomica.virial.cluster.VirialDiagramsMix
-
- VirialDiagramsMix2 - Class in etomica.virial.cluster
-
- VirialDiagramsMix2(int, boolean[]) - Constructor for class etomica.virial.cluster.VirialDiagramsMix2
-
- VirialDiagramsMix2(int, boolean[], boolean) - Constructor for class etomica.virial.cluster.VirialDiagramsMix2
-
- VirialDiagramsMix2.MaxIsomorphCriteriaMixture - Class in etomica.virial.cluster
-
- VirialDiagramsPT - Class in etomica.virial.cluster
-
- VirialDiagramsPT(int, boolean, boolean) - Constructor for class etomica.virial.cluster.VirialDiagramsPT
-
- VirialDiagramsPT(int, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.VirialDiagramsPT
-
- VirialDiagramsPT.ArticulatedAt0 - Class in etomica.virial.cluster
-
- VirialDiagramsPT.ComparatorNumFieldNodesExchange - Class in etomica.virial.cluster
-
- VirialDiagramsPT.DiscardCriteria - Class in etomica.virial.cluster
-
- VirialEmulNonAdditive - Class in etomica.virial.simulations
-
- VirialEmulNonAdditive() - Constructor for class etomica.virial.simulations.VirialEmulNonAdditive
-
- VirialEmulNonAdditive.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialExternalFieldConfinedOverlap - Class in etomica.virial.simulations
-
External Field simulation using Overlap2 sampling to evaluate cluster integrals
- VirialExternalFieldConfinedOverlap() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlap
-
- VirialExternalFieldConfinedOverlap.VirialExternalFieldParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialExternalFieldConfinedOverlapRho - Class in etomica.virial.simulations
-
External Field simulation using Overlap2 sampling to evaluate cluster integrals
- VirialExternalFieldConfinedOverlapRho() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho
-
- VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialExternalFieldConfinedOverlapSW - Class in etomica.virial.simulations
-
External Field simulation using Overlap2 sampling to evaluate cluster integrals
- VirialExternalFieldConfinedOverlapSW() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW
-
- VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialExternalFieldOverlapRho - Class in etomica.virial.simulations
-
External Field simulation using Overlap2 sampling to evaluate cluster integrals
- VirialExternalFieldOverlapRho() - Constructor for class etomica.virial.simulations.VirialExternalFieldOverlapRho
-
- VirialExternalFieldOverlapRho.VirialExternalFieldParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialExternalFieldParam() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
-
- VirialExternalFieldParam() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
-
- VirialExternalFieldParam() - Constructor for class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
-
- VirialExternalFieldParam() - Constructor for class etomica.virial.simulations.VirialExternalFieldOverlapRho.VirialExternalFieldParam
-
- VirialGCPM - Class in etomica.virial.simulations
-
- VirialGCPM() - Constructor for class etomica.virial.simulations.VirialGCPM
-
- VirialGCPM.VirialGCPMParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialGCPMGraphic - Class in etomica.virial.simulations
-
- VirialGCPMGraphic() - Constructor for class etomica.virial.simulations.VirialGCPMGraphic
-
- VirialGCPMParam() - Constructor for class etomica.virial.simulations.VirialGCPM.VirialGCPMParam
-
- VirialH2O - Class in etomica.virial.simulations
-
- VirialH2O() - Constructor for class etomica.virial.simulations.VirialH2O
-
- VirialH2O.VirialH2OParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialH2OGCPMD - Class in etomica.virial.simulations
-
Computes virial coefficients and its temperature derivatives for GCPM Water
- VirialH2OGCPMD() - Constructor for class etomica.virial.simulations.VirialH2OGCPMD
-
- VirialH2OGCPMD.Clusterfoo - Class in etomica.virial.simulations
-
- VirialH2OGCPMD.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialH2OParam() - Constructor for class etomica.virial.simulations.VirialH2O.VirialH2OParam
-
- VirialH2PI - Class in etomica.virial.simulations
-
Mayer sampling simulation
- VirialH2PI() - Constructor for class etomica.virial.simulations.VirialH2PI
-
- VirialH2PI.VirialH2PIParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialH2PIBoltzmann - Class in etomica.virial.simulations
-
- VirialH2PIBoltzmann() - Constructor for class etomica.virial.simulations.VirialH2PIBoltzmann
-
- VirialH2PIBoltzmann.VirialHePIParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialH2PIParam() - Constructor for class etomica.virial.simulations.VirialCO2PI.VirialH2PIParam
-
- VirialH2PIParam() - Constructor for class etomica.virial.simulations.VirialH2PI.VirialH2PIParam
-
- VirialH2PISimple - Class in etomica.virial.simulations
-
- VirialH2PISimple() - Constructor for class etomica.virial.simulations.VirialH2PISimple
-
- VirialH2PISimple.VirialH2PISimpleParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialH2PISimpleParam() - Constructor for class etomica.virial.simulations.VirialH2PISimple.VirialH2PISimpleParam
-
- VirialH2PIXC - Class in etomica.virial.simulations
-
- VirialH2PIXC() - Constructor for class etomica.virial.simulations.VirialH2PIXC
-
- VirialH2PIXC.VirialHePIParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialH2PYCorrection - Class in etomica.virial.simulations
-
Computes corrections to Percus-Yevick approximations of B4 and B5 for a hydrogen pair potential.
- VirialH2PYCorrection() - Constructor for class etomica.virial.simulations.VirialH2PYCorrection
-
- VirialH2PYCorrection.VirialH2PYCParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialH2PYCParam() - Constructor for class etomica.virial.simulations.VirialH2PYCorrection.VirialH2PYCParam
-
- VirialHardAssociationCone - Class in etomica.virial.simulations
-
Virial coefficients with single attraction site AssociationCone Potential using Mayer Sampling
- VirialHardAssociationCone() - Constructor for class etomica.virial.simulations.VirialHardAssociationCone
-
- VirialHardAssociationCone.VirialLJParam - Class in etomica.virial.simulations
-
- VirialHardAssociationConeDoubleSites - Class in etomica.virial.simulations
-
Virial coefficients with double attraction site AssociationCone Potential using Mayer Sampling
- VirialHardAssociationConeDoubleSites() - Constructor for class etomica.virial.simulations.VirialHardAssociationConeDoubleSites
-
- VirialHardAssociationConeDoubleSites.VirialLJParam - Class in etomica.virial.simulations
-
- VirialHeNonAdditive - Class in etomica.virial.simulations
-
- VirialHeNonAdditive() - Constructor for class etomica.virial.simulations.VirialHeNonAdditive
-
- VirialHeNonAdditive.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHeNonAdditiveWheatley - Class in etomica.virial.simulations
-
Adapted by Andrew from VirialHeNonAdditive
Computes only the nonadditive component of either the third, fourth, or fifth virial coefficient for the
ab initio non-additive trimer potential for He developed by Cencek, Patkowski, and Szalewicz (JCP 131 064105 2009).
- VirialHeNonAdditiveWheatley() - Constructor for class etomica.virial.simulations.VirialHeNonAdditiveWheatley
-
- VirialHeNonAdditiveWheatley.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHePCKLJS - Class in etomica.virial.simulations
-
Computes additive virial coefficients using the pair potential for He of Przybytek et al.
- VirialHePCKLJS() - Constructor for class etomica.virial.simulations.VirialHePCKLJS
-
- VirialHePCKLJS.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHePCKLJSCHNCCorrection - Class in etomica.virial.simulations
-
Computes corrections to hypernetted-chain approximations of B4 and B5 for a helium pair potential.
- VirialHePCKLJSCHNCCorrection() - Constructor for class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection
-
- VirialHePCKLJSCHNCCorrection.VirialLJParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHePCKLJSPYCorrection - Class in etomica.virial.simulations
-
Computes corrections to Percus-Yevick approximations of B4 and B5 for a helium pair potential.
- VirialHePCKLJSPYCorrection() - Constructor for class etomica.virial.simulations.VirialHePCKLJSPYCorrection
-
- VirialHePCKLJSPYCorrection.VirialLJParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHePCKLJSTempDeriv - Class in etomica.virial.simulations
-
Computes first or second temperatures (see firstDerivative variable) of additive virial coefficients using the
ab initio pair potential for helium from Przybytek et al.
- VirialHePCKLJSTempDeriv() - Constructor for class etomica.virial.simulations.VirialHePCKLJSTempDeriv
-
- VirialHePCKLJSTempDeriv.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHePI - Class in etomica.virial.simulations
-
Mayer sampling simulation
- VirialHePI() - Constructor for class etomica.virial.simulations.VirialHePI
-
- VirialHePI.FlexApproach - Enum in etomica.virial.simulations
-
- VirialHePI.VirialHePIParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHePI_PotentialCorrection - Class in etomica.virial.simulations
-
Mayer sampling simulation
- VirialHePI_PotentialCorrection() - Constructor for class etomica.virial.simulations.VirialHePI_PotentialCorrection
-
- VirialHePI_PotentialCorrection.VirialHePIParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHePIGraphic - Class in etomica.virial.simulations
-
Mayer sampling simulation
- VirialHePIGraphic() - Constructor for class etomica.virial.simulations.VirialHePIGraphic
-
- VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialH2PIBoltzmann.VirialHePIParam
-
- VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialH2PIXC.VirialHePIParam
-
- VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialHePI.VirialHePIParam
-
- VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialHePI_PotentialCorrection.VirialHePIParam
-
- VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialHePIXC.VirialHePIParam
-
- VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialHePIXCEven.VirialHePIParam
-
- VirialHePIParam() - Constructor for class etomica.virial.simulations.VirialHePIXCOdd.VirialHePIParam
-
- VirialHePIXC - Class in etomica.virial.simulations
-
Mayer sampling simulation for alkanes using the TraPPE force field.
- VirialHePIXC() - Constructor for class etomica.virial.simulations.VirialHePIXC
-
- VirialHePIXC.VirialHePIParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHePIXCEven - Class in etomica.virial.simulations
-
MSMC calculation for the "even" exchange component of helium-4 virial coefficients.
- VirialHePIXCEven() - Constructor for class etomica.virial.simulations.VirialHePIXCEven
-
- VirialHePIXCEven.VirialHePIParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHePIXCOdd - Class in etomica.virial.simulations
-
MSMC calculation for pieces of the "odd" exchange component of helium-4 virial coefficients.
- VirialHePIXCOdd() - Constructor for class etomica.virial.simulations.VirialHePIXCOdd
-
- VirialHePIXCOdd.VirialHePIParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHePYCorrection - Class in etomica.virial.simulations
-
Computes corrections to Percus-Yevick approximations of B4 and B5 for a helium pair potential.
- VirialHePYCorrection() - Constructor for class etomica.virial.simulations.VirialHePYCorrection
-
- VirialHePYCorrection.VirialHePYCParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHePYCParam() - Constructor for class etomica.virial.simulations.VirialHePYCorrection.VirialHePYCParam
-
- VirialHePYCParam() - Constructor for class etomica.virial.simulations.VirialHeSC.VirialHePYCParam
-
- VirialHeSC - Class in etomica.virial.simulations
-
Computes virial coefficients for a helium pair potential.
- VirialHeSC() - Constructor for class etomica.virial.simulations.VirialHeSC
-
- VirialHeSC.VirialHePYCParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHS - Class in etomica.virial.simulations
-
Calculation for virial coefficients of hard spheres
- VirialHS() - Constructor for class etomica.virial.simulations.VirialHS
-
- VirialHS.VirialHSParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHSBinMultiThreaded - Class in etomica.virial.simulations
-
Calculation for virial coefficients of hard spheres
- VirialHSBinMultiThreaded() - Constructor for class etomica.virial.simulations.VirialHSBinMultiThreaded
-
- VirialHSBinMultiThreaded.DooDad - Class in etomica.virial.simulations
-
- VirialHSBinMultiThreaded.SimulationWorker - Class in etomica.virial.simulations
-
- VirialHSBinMultiThreaded.VirialHSBinParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHSBinParam() - Constructor for class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- VirialHSBinParam() - Constructor for class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- VirialHSMixture - Class in etomica.virial.simulations
-
Calculation for virial coefficients of hard sphere mixture
- VirialHSMixture() - Constructor for class etomica.virial.simulations.VirialHSMixture
-
- VirialHSMixture.VirialHSParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHSOrC - Class in etomica.virial.simulations
-
Overlap sampling simulation to compute c(r) for HS
- VirialHSOrC() - Constructor for class etomica.virial.simulations.VirialHSOrC
-
- VirialHSOrC.PotentialChoice - Enum in etomica.virial.simulations
-
- VirialHSOrC.VirialLJrParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialHSParam() - Constructor for class etomica.virial.simulations.VirialHS.VirialHSParam
-
- VirialHSParam() - Constructor for class etomica.virial.simulations.VirialHSMixture.VirialHSParam
-
- VirialHSParam() - Constructor for class etomica.virial.simulations.VirialPolyhedra.VirialHSParam
-
- VirialHSParam() - Constructor for class etomica.virial.simulations.VirialPolyhedra2.VirialHSParam
-
- VirialHSParam() - Constructor for class etomica.virial.simulations.VirialSQWBinMultiRecalcW.VirialHSParam
-
- VirialHSParam() - Constructor for class etomica.virial.simulations.VirialSQWRecalcSmallMem.VirialHSParam
-
- VirialLJ - Class in etomica.virial.simulations
-
LJ simulation using Mayer sampling to evaluate cluster integrals
- VirialLJ() - Constructor for class etomica.virial.simulations.VirialLJ
-
- VirialLJ.VirialLJParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialLJBridge - Class in etomica.virial.simulations
-
MSMC computations (via overlap sampling) of the bridge diagram(s) within the
f-bond-only formulation.
- VirialLJBridge() - Constructor for class etomica.virial.simulations.VirialLJBridge
-
- VirialLJBridge.VirialLJParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialLJCHNCCorrection - Class in etomica.virial.simulations
-
LJ simulation using Mayer sampling to evaluate corrections to the HNC(c) approximations to B4 and B5
- VirialLJCHNCCorrection() - Constructor for class etomica.virial.simulations.VirialLJCHNCCorrection
-
- VirialLJCHNCCorrection.VirialLJParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialLJD - Class in etomica.virial.simulations
-
LJ simulation using Mayer sampling to evaluate cluster integrals
- VirialLJD() - Constructor for class etomica.virial.simulations.VirialLJD
-
- VirialLJD.VirialLJParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialLJMultiOverlap - Class in etomica.virial.simulations
-
LJ simulation using Mayer sampling to evaluate cluster integrals
- VirialLJMultiOverlap() - Constructor for class etomica.virial.simulations.VirialLJMultiOverlap
-
- VirialLJMultiOverlap.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialLJOrC - Class in etomica.virial.simulations
-
LJ simulation using Mayer sampling to evaluate cluster integrals
- VirialLJOrC() - Constructor for class etomica.virial.simulations.VirialLJOrC
-
- VirialLJOrC.PotentialChoice - Enum in etomica.virial.simulations
-
- VirialLJOrC.VirialLJrParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialLJOrICPYC - Class in etomica.virial.simulations
-
LJ simulation using Mayer sampling to evaluate cluster integrals
- VirialLJOrICPYC() - Constructor for class etomica.virial.simulations.VirialLJOrICPYC
-
- VirialLJOrICPYC.VirialLJrParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialLJParam() - Constructor for class etomica.virial.simulations.DirectSamplingTargetQCArReferenceAzizAr.VirialLJParam
-
- VirialLJParam() - Constructor for class etomica.virial.simulations.LJTSRefLJ.VirialLJParam
-
- VirialLJParam() - Constructor for class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
-
- VirialLJParam() - Constructor for class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
-
- VirialLJParam() - Constructor for class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- VirialLJParam() - Constructor for class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- VirialLJParam() - Constructor for class etomica.virial.simulations.VirialLJ.VirialLJParam
-
- VirialLJParam() - Constructor for class etomica.virial.simulations.VirialLJBridge.VirialLJParam
-
- VirialLJParam() - Constructor for class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
-
- VirialLJParam() - Constructor for class etomica.virial.simulations.VirialLJD.VirialLJParam
-
- VirialLJParam() - Constructor for class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
-
- VirialLJParam() - Constructor for class etomica.virial.simulations.VirialLJSeries.VirialLJParam
-
- VirialLJPYCorrection - Class in etomica.virial.simulations
-
LJ simulation using Mayer sampling to evaluate corrections to the PY(c) approximations to B4 and B5
- VirialLJPYCorrection() - Constructor for class etomica.virial.simulations.VirialLJPYCorrection
-
- VirialLJPYCorrection.VirialLJParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialLJQB2 - Class in etomica.modules.vle
-
LJ simulation using Mayer sampling to evaluate cluster integrals
- VirialLJQB2() - Constructor for class etomica.modules.vle.VirialLJQB2
-
- VirialLJrParam() - Constructor for class etomica.virial.simulations.VirialHSOrC.VirialLJrParam
-
- VirialLJrParam() - Constructor for class etomica.virial.simulations.VirialLJOrC.VirialLJrParam
-
- VirialLJrParam() - Constructor for class etomica.virial.simulations.VirialLJOrICPYC.VirialLJrParam
-
- VirialLJSeries - Class in etomica.virial.simulations
-
LJ simulation using Mayer sampling to integrals that show up in series
expansion.
- VirialLJSeries() - Constructor for class etomica.virial.simulations.VirialLJSeries
-
- VirialLJSeries.VirialLJParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialMethaneEH - Class in etomica.virial.simulations
-
TraPPE-EH methane, CH4
Mayer sampling to evaluate cluster integrals
- VirialMethaneEH() - Constructor for class etomica.virial.simulations.VirialMethaneEH
-
- VirialMethaneEH.VirialMethaneParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialMethaneParam() - Constructor for class etomica.virial.simulations.VirialMethaneEH.VirialMethaneParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCH4AlkaneEHMix.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2AlkaneEHMix.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2AlkaneUAMix.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2CH4Mix.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2CH4UAMix.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2CH4UAMixWheatley.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialCO2N2Mix.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialLJMultiOverlap.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialN2AlkaneEHMix.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialN2AlkaneUAMix.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialN2AlkaneUARigid.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialN2CH4Mix.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialN2CH4UAMix.VirialMixParam
-
- VirialMixParam() - Constructor for class etomica.virial.simulations.VirialSF6LJAlkaneUAMix.VirialMixParam
-
- VirialN2 - Class in etomica.virial.simulations
-
- VirialN2() - Constructor for class etomica.virial.simulations.VirialN2
-
- VirialN2.VirialN2Param - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialN2AlkaneEHMix - Class in etomica.virial.simulations
-
Mayer sampling simulation for N2(rigid, TraPPE)-alkanes(TraPPE-EH) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=1])
- VirialN2AlkaneEHMix() - Constructor for class etomica.virial.simulations.VirialN2AlkaneEHMix
-
- VirialN2AlkaneEHMix.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialN2AlkaneUAMix - Class in etomica.virial.simulations
-
Mayer sampling simulation for N2(rigid, TraPPE)-alkanes(TraPPE-UA) mixture
Martin and Siepmann, JPC(B) 102, 2569-2577 (1998)
eovererr can be used
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
see "VirialN2AlkaneUARigid" B11 code(use rigid mix diagram)
rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=1])
- VirialN2AlkaneUAMix() - Constructor for class etomica.virial.simulations.VirialN2AlkaneUAMix
-
- VirialN2AlkaneUAMix.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialN2AlkaneUARigid - Class in etomica.virial.simulations
-
cross virial coefficients of mixture of N2 and alkanes(TraPPE-UA)
no flexible diagrams, just rigid diagrams
just for B11, see "VirialN2AlkaneMix" for flexible corrections
N2:use CO2EMP, C<==> "A", O<==>"N"
- VirialN2AlkaneUARigid() - Constructor for class etomica.virial.simulations.VirialN2AlkaneUARigid
-
- VirialN2AlkaneUARigid.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialN2CH4Mix - Class in etomica.virial.simulations
-
Mayer sampling simulation for N2(rigid, TraPPE)-CH4(TraPPE-EH) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams
- VirialN2CH4Mix() - Constructor for class etomica.virial.simulations.VirialN2CH4Mix
-
- VirialN2CH4Mix.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialN2CH4UAMix - Class in etomica.virial.simulations
-
Mayer sampling simulation for N2(rigid, TraPPE)-CH4(rigid, TraPPE-UA) mixture
cross virial coefficients
Using VirialDiagramMix2 to generate diagrams
rigid diagrams only since both of the components are rigid
- VirialN2CH4UAMix() - Constructor for class etomica.virial.simulations.VirialN2CH4UAMix
-
- VirialN2CH4UAMix.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialN2Param() - Constructor for class etomica.virial.simulations.VirialN2.VirialN2Param
-
- VirialN2Param() - Constructor for class etomica.virial.simulations.VirialN2PI.VirialN2Param
-
- VirialN2Param() - Constructor for class etomica.virial.simulations.VirialN2TraPPE.VirialN2Param
-
- VirialN2PI - Class in etomica.virial.simulations
-
- VirialN2PI() - Constructor for class etomica.virial.simulations.VirialN2PI
-
- VirialN2PI.VirialN2Param - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialN2TraPPE - Class in etomica.virial.simulations
-
TraPPE N2 model
Potoff and Siepmann.
- VirialN2TraPPE() - Constructor for class etomica.virial.simulations.VirialN2TraPPE
-
- VirialN2TraPPE.VirialN2Param - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialNaphthaleneTraPPE - Class in etomica.virial.simulations
-
TraPPE Naphthalene model , pure
LJ no electrostatic
Mayer sampling to evaluate cluster integrals
reference: TraPPE 4, Siepmann
- VirialNaphthaleneTraPPE() - Constructor for class etomica.virial.simulations.VirialNaphthaleneTraPPE
-
- VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam - Class in etomica.virial.simulations
-
6
Inner class for parameters
- VirialNaphthaleneTraPPEParam() - Constructor for class etomica.virial.simulations.VirialNaphthaleneTraPPE.VirialNaphthaleneTraPPEParam
-
- virialNonAdditiveTrimerEnergy(int, MayerFunction, Potential, boolean, boolean) - Static method in class etomica.virial.cluster.Standard
-
- VirialO2 - Class in etomica.virial.simulations
-
- VirialO2() - Constructor for class etomica.virial.simulations.VirialO2
-
- VirialO2.VirialO2Param - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialO2Param() - Constructor for class etomica.virial.simulations.VirialO2.VirialO2Param
-
- VirialO2Param() - Constructor for class etomica.virial.simulations.VirialO2PI.VirialO2Param
-
- VirialO2PI - Class in etomica.virial.simulations
-
- VirialO2PI() - Constructor for class etomica.virial.simulations.VirialO2PI
-
- VirialO2PI.VirialO2Param - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialOptimizer - Class in etomica.math.numerical
-
Class to determine B9 value that best fit the simulation results after
Pade Approximation [K/L]
- VirialOptimizer(String, String) - Constructor for class etomica.math.numerical.VirialOptimizer
-
- VirialOptimizer.VirialParam - Class in etomica.math.numerical
-
- VirialParam() - Constructor for class etomica.math.numerical.PadeApproximation.VirialParam
-
- VirialParam() - Constructor for class etomica.math.numerical.VirialOptimizer.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.BnFlexibleContributionTraPPEUAMethanol.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.ReeHooverMC.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialAceticAcid.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialAceticAcidFlex.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialAlkaneEHTest.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialB2WaterTIP4P_DHS_difference.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialB3C1HSDipole.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialB3C1TIP4Pwater.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialB3C2HSDipole.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialB3C2TIP4Pwater.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialCO2H2OGCPM.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialCO2H2OGCPMX.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialEmulNonAdditive.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialH2OGCPMD.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialHeNonAdditive.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialHeNonAdditiveWheatley.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialHePCKLJS.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialRowleyAlcohol.VirialParam
-
- VirialParam() - Constructor for class etomica.virial.simulations.VirialTraPPEAlcohol.VirialParam
-
- VirialPh3site464Param() - Constructor for class etomica.virial.simulations.VirialPh464.VirialPh3site464Param
-
- VirialPh3site545Param() - Constructor for class etomica.virial.simulations.VirialPh545.VirialPh3site545Param
-
- VirialPh464 - Class in etomica.virial.simulations
-
Phenanthrene model , pure
support for CO2/phenanthrene mixture calculation
3 site model from Iwai this is 464 model
Mayer sampling to evaluate cluster integrals
- VirialPh464() - Constructor for class etomica.virial.simulations.VirialPh464
-
- VirialPh464.VirialPh3site464Param - Class in etomica.virial.simulations
-
6
Inner class for parameters
- VirialPh545 - Class in etomica.virial.simulations
-
Phenanthrene model , pure
support for CO2/phenanthrene mixture calculation
3 site model from Iwai this is 545 model
Mayer sampling to evaluate cluster integrals
- VirialPh545() - Constructor for class etomica.virial.simulations.VirialPh545
-
- VirialPh545.VirialPh3site545Param - Class in etomica.virial.simulations
-
6
Inner class for parameters
- VirialPhenanthreneTraPPE - Class in etomica.virial.simulations
-
TraPPE phenanthrene model , pure
LJ no electrostatic
Mayer sampling to evaluate cluster integrals
reference: TraPPE 4, Siepmann
- VirialPhenanthreneTraPPE() - Constructor for class etomica.virial.simulations.VirialPhenanthreneTraPPE
-
- VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialPhenanthreneTraPPEParam() - Constructor for class etomica.virial.simulations.VirialPhenanthreneTraPPE.VirialPhenanthreneTraPPEParam
-
- VirialPolyhedra - Class in etomica.virial.simulations
-
Calculation for virial coefficients of hard spheres
- VirialPolyhedra() - Constructor for class etomica.virial.simulations.VirialPolyhedra
-
- VirialPolyhedra.DataProcessorR2 - Class in etomica.virial.simulations
-
- VirialPolyhedra.VirialHSParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialPolyhedra2 - Class in etomica.virial.simulations
-
Calculation for virial coefficients of hard spheres
- VirialPolyhedra2() - Constructor for class etomica.virial.simulations.VirialPolyhedra2
-
- VirialPolyhedra2.DataProcessorR2 - Class in etomica.virial.simulations
-
- VirialPolyhedra2.VirialHSParam - Class in etomica.virial.simulations
-
Inner class for parameters
- virialProfile - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- virialProfileWork - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- VirialRowleyAlcohol - Class in etomica.virial.simulations
-
Mayer-sampling MC simulation for methanol or ethanol using the potentials published in:
R.L.
- VirialRowleyAlcohol() - Constructor for class etomica.virial.simulations.VirialRowleyAlcohol
-
- VirialRowleyAlcohol.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- virialSeriesCluster(int, MayerFunction[], int[]) - Static method in class etomica.virial.cluster.Standard
-
- VirialSF6LJAlkaneUAMix - Class in etomica.virial.simulations
-
Mayer sampling simulation for SF6(rigid, LJ sphere)-alkanes(TraPPE-UA) mixture cross virial coefficients
eovererr can be used
Using VirialDiagramMix2 to generate diagrams
rigid diagrams and flex diagrams are calculated respectively(Bij = Bij[flexID=-1] + Bij[flexID=0])
- VirialSF6LJAlkaneUAMix() - Constructor for class etomica.virial.simulations.VirialSF6LJAlkaneUAMix
-
- VirialSF6LJAlkaneUAMix.VirialMixParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialSF6Param() - Constructor for class etomica.virial.simulations.Virial7SiteRigidSF6.VirialSF6Param
-
- VirialSiepmannSpheresParam() - Constructor for class etomica.virial.simulations.VirialAlkane.VirialSiepmannSpheresParam
-
- VirialSiepmannSpheresParam() - Constructor for class etomica.virial.simulations.VirialAlkaneFlex.VirialSiepmannSpheresParam
-
- VirialSiepmannSpheresParam() - Constructor for class etomica.virial.simulations.VirialAlkaneFull.VirialSiepmannSpheresParam
-
- VirialSiepmannSpheresParam() - Constructor for class etomica.virial.simulations.VirialAlkaneSKS.VirialSiepmannSpheresParam
-
- VirialSiepmannSpheresParam() - Constructor for class etomica.virial.simulations.VirialSwsPT.VirialSiepmannSpheresParam
-
- VirialSQWBinMultiRecalcW - Class in etomica.virial.simulations
-
Calculation for virial coefficients of hard spheres
- VirialSQWBinMultiRecalcW() - Constructor for class etomica.virial.simulations.VirialSQWBinMultiRecalcW
-
- VirialSQWBinMultiRecalcW.VirialHSParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialSQWBinMultiThreaded - Class in etomica.virial.simulations
-
Calculation for virial coefficients of hard spheres
- VirialSQWBinMultiThreaded() - Constructor for class etomica.virial.simulations.VirialSQWBinMultiThreaded
-
- VirialSQWBinMultiThreaded.SimulationWorker - Class in etomica.virial.simulations
-
- VirialSQWBinMultiThreaded.VirialHSBinParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialSQWRecalcSmallMem - Class in etomica.virial.simulations
-
Calculation for virial coefficients of hard spheres
- VirialSQWRecalcSmallMem() - Constructor for class etomica.virial.simulations.VirialSQWRecalcSmallMem
-
- VirialSQWRecalcSmallMem.VirialHSParam - Class in etomica.virial.simulations
-
Inner class for parameters
- virialSum - Variable in class etomica.data.meter.MeterPressureHard
-
- virialSum - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLat.ReturnValue
-
- virialSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuper
-
- virialSum - Variable in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- virialSumCO - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- virialSumCO2 - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- virialSumIG - Variable in class etomica.modules.mu.DataSourceWallPressureMu
-
- virialSumO2 - Variable in class etomica.modules.catalysis.DataSourceWallPressureCatalysis
-
- virialSumSQW - Variable in class etomica.modules.mu.DataSourceWallPressureMu
-
- VirialSW - Class in etomica.virial.simulations
-
SW simulation using Mayer sampling to evaluate cluster integrals
- VirialSW() - Constructor for class etomica.virial.simulations.VirialSW
-
- VirialSW.VirialSWParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialSWParam() - Constructor for class etomica.virial.simulations.VirialSW.VirialSWParam
-
- VirialSwsPT - Class in etomica.virial.simulations
-
- VirialSwsPT() - Constructor for class etomica.virial.simulations.VirialSwsPT
-
- VirialSwsPT.VirialSiepmannSpheresParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialSWWE - Class in etomica.virial.simulations
-
- VirialSWWE() - Constructor for class etomica.virial.simulations.VirialSWWE
-
- VirialSWWE.VirialSWWEParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialSWWEParam() - Constructor for class etomica.virial.simulations.VirialSWWE.VirialSWWEParam
-
- VirialTraPPEAlcohol - Class in etomica.virial.simulations
-
Mayer-sampling MC simulation for methanol or ethanol using the TraPPE model: http://www.chem.umn.edu/groups/siepmann/trappe/intro.php
Set species, model (with or without point charges), virial-coefficent type (B2, B3, etc.),
and temperature in VirialParam() method at bottom of file.
- VirialTraPPEAlcohol() - Constructor for class etomica.virial.simulations.VirialTraPPEAlcohol
-
- VirialTraPPEAlcohol.VirialParam - Class in etomica.virial.simulations
-
Inner class for parameters
- VirialWaterOverlap - Class in etomica.virial.simulations
-
Generic simulation using Mayer sampling to evaluate cluster integrals
- VirialWaterOverlap() - Constructor for class etomica.virial.simulations.VirialWaterOverlap
-
- Viscosity - Class in etomica.units.dimensions
-
Dimension for all units of viscosity, Mass/(Length-Time)
- viscosity() - Method in class etomica.units.systems.CGS
-
- viscosity() - Method in class etomica.units.systems.LJ
-
- viscosity() - Method in class etomica.units.systems.MKS
-
- viscosity() - Method in class etomica.units.systems.UnitSystem.Sim
-
- viscosity() - Method in class etomica.units.systems.UnitSystem
-
- visit(Edge) - Method in interface etomica.graph.model.EdgeVisitor
-
- visit(Node) - Method in interface etomica.graph.model.NodeVisitor
-
- visit(byte) - Method in class etomica.graph.traversal.AbstractTraversal
-
- visit(byte, byte) - Method in class etomica.graph.traversal.BCVisitor
-
- visit(byte, byte) - Method in class etomica.graph.traversal.CVisitor
-
- visit(byte, byte) - Method in interface etomica.graph.traversal.TraversalVisitor
-
- visited - Variable in class etomica.graph.traversal.Biconnected
-
- visitEdges(EdgeVisitor) - Method in interface etomica.graph.model.Graph
-
- visitEdges(EdgeVisitor) - Method in class etomica.graph.model.impl.GraphImpl
-
- visitNodes(NodeVisitor) - Method in interface etomica.graph.model.Graph
-
- visitNodes(NodeVisitor) - Method in class etomica.graph.model.impl.GraphImpl
-
- visualrange - Static variable in class org.jmol.script.Token
-
- VLE - Class in etomica.modules.vle
-
- VLE(VLESim, Space) - Constructor for class etomica.modules.vle.VLE
-
- VLE.Applet - Class in etomica.modules.vle
-
- VLESim - Class in etomica.modules.vle
-
- VLESim() - Constructor for class etomica.modules.vle.VLESim
-
- vmax - Variable in class etomica.modules.clustergenerator.Plot
-
- vmin - Variable in class etomica.modules.clustergenerator.Plot
-
- vN2Angles(double, double, double, double) - Method in class etomica.potential.P2NitrogenHellmann
-
- vNew - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- vNew - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- Vnlll - Variable in class etomica.potential.P2HydrogenPatkowski
-
- Vnlll - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- vOH - Variable in class etomica.integrator.mcmove.MCMoveTorsionAceticAcid
-
- vOH - Variable in class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- vol - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- vol - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- vol - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- vol - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- vOld - Variable in class etomica.modules.adsorption.P1Wall
-
- vOld - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- Volt - Class in etomica.units
-
The Volt unit of electric potential.
- volume() - Method in class etomica.modules.pistoncylinder.BoundaryPistonCylinder
-
- volume - Variable in class etomica.normalmode.DataSourceAvgPressure2
-
- volume - Variable in class etomica.normalmode.DataSourceMuRoot
-
- volume - Variable in class etomica.normalmode.DataSourceMuRoot1
-
- volume - Variable in class etomica.normalmode.DataSourceMuRootPMatch
-
- volume - Variable in class etomica.normalmode.DataSourcePMu
-
- volume - Variable in class etomica.normalmode.MeterSolidProps
-
- volume - Variable in class etomica.normalmode.MeterSolidPropsLJ
-
- volume - Variable in class etomica.normalmode.PotentialCalculationEFSSP
-
- volume - Variable in class etomica.normalmode.PotentialCalculationLJSP
-
- volume - Variable in class etomica.potential.EwaldSummation
-
- volume - Variable in class etomica.potential.EwaldSumMolecules
-
- volume() - Method in class etomica.space.Boundary
-
- volume() - Method in class etomica.space.BoundaryDeformablePeriodic
-
- volume() - Method in class etomica.space.BoundaryRectangular
-
Returns the "volume" of the rectangular region defined by this Boundary.
- Volume - Class in etomica.units.dimensions
-
Dimension for all volume units.
- volume() - Method in class etomica.units.systems.CGS
-
- volume() - Method in class etomica.units.systems.LJ
-
- volume() - Method in class etomica.units.systems.MKS
-
- volume() - Method in class etomica.units.systems.UnitSystem.Sim
-
- volume() - Method in class etomica.units.systems.UnitSystem
-
- volume - Variable in class etomica.virial.simulations.ShapeParser.ShapeData
-
- volume - Static variable in class org.jmol.script.Token
-
- VolumeBias(double, int) - Constructor for class etomica.liquidLJ.LjMd3D.VolumeBias
-
- volumeChanges - Variable in class etomica.modules.ensembles.LJMCGraphic
-
- volumeChanges - Variable in class etomica.modules.statistics.StatisticsMCGraphic
-
- volumeRender(boolean) - Method in class org.jmol.g3d.Graphics3D
-
- volumeRender4(int, int, int, int) - Method in class org.jmol.g3d.Graphics3D
-
- vp(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
-
- vp(double, double) - Method in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
-
- vp(double, double) - Method in interface etomica.mappedvirial.PotentialCalculationMappedVirialV.VFunc
-
- vScale - Variable in class etomica.integrator.mcmove.MCMoveVolume
-
- vScale - Variable in class etomica.normalmode.MCMoveVolumeSolidNPTMolecular
-
- vShift - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- vShift - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- vShift - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- vShift - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.UShift
-
- vShift - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV.USine
-
- vShift - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- vSource - Variable in class etomica.mappedvirial.MappedVirialLJVGr.LJMDParams
-
- vSums - Variable in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
- vTot - Variable in class etomica.freeenergy.npath.IntegratorImageHarmonicMD
-
- vTot - Variable in class etomica.freeenergy.npath.IntegratorMDHarmonicMC
-
W
- w - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
-
- w - Variable in class etomica.freeenergy.npath.SimFe.LjMC3DParams
-
- w - Variable in class etomica.freeenergy.npath.SimIdealGas.LjMC3DParams
-
- w - Variable in class etomica.freeenergy.npath.SimLattice.LjMC3DParams
-
- w - Variable in class etomica.freeenergy.npath.SimLJ.LjMC3DParams
-
- w - Variable in class etomica.meam.EFSTungsten
-
- w - Variable in class etomica.modules.materialfracture.P1Tension
-
- W - Variable in class etomica.modules.rheology.IntegratorPolymer
-
- w - Variable in class etomica.potential.P2SpheroPolyhedron
-
- w - Variable in class etomica.potential.P3HydrogenManzhos
-
- w - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.SimulationWorker
-
- w - Variable in class etomica.virial.simulations.VirialHSBinMultiThreaded.VirialHSBinParam
-
- w - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.SimulationWorker
-
- w - Variable in class etomica.virial.simulations.VirialSQWBinMultiThreaded.VirialHSBinParam
-
- w - Variable in class org.jmol.util.Tuple4f
-
The w coordinate.
- W0 - Variable in class etomica.potential.P2SpheroPolyhedron
-
- W1 - Variable in class etomica.potential.P2SpheroPolyhedron
-
- W2 - Variable in class etomica.potential.P2SpheroPolyhedron
-
- w3j - Variable in class etomica.potential.P2HydrogenPatkowski
-
- w3j - Variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- wA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
-
- wA - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
-
- waitformoveto - Static variable in class org.jmol.script.Token
-
- WaitObject() - Constructor for class etomica.action.activity.Controller.WaitObject
-
- walk(Graph, List<Byte>, byte, byte, byte) - Method in class etomica.graph.property.FFTDecomposition
-
- walk(Graph, List<Byte>, byte, byte, byte) - Method in class etomica.graph.property.IsFFT
-
- walkDimer() - Method in class etomica.dimer.IntegratorDimerMin
-
Moves the half-dimer stepLength*N towards the energy minimum.
- wallButton - Variable in class etomica.modules.sam.SamGraphic
-
- wallDim - Variable in class etomica.modules.dcvgcmd.P1WCAWall
-
- wallDim - Variable in class etomica.modules.sam.P1WCAWall
-
- walldistance - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlap.VirialExternalFieldParam
-
- walldistance - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapRho.VirialExternalFieldParam
-
- walldistance - Variable in class etomica.virial.simulations.VirialExternalFieldConfinedOverlapSW.VirialExternalFieldParam
-
- wallForce - Variable in class etomica.modules.rosmosis.PotentialCalculationForceSumWallForce
-
- wallForce - Variable in class etomica.modules.rosmosis.PotentialCalculationTorqueSumWallForce
-
- wallForceSum - Variable in class etomica.modules.sam.PotentialCalculationForceSumWall
-
- WallPlane - Class in etomica.modules.sam
-
Wrap a P1WCAWall and make it look like a Plane.
- WallPlane(Space, P1WCAWall) - Constructor for class etomica.modules.sam.WallPlane
-
- wallPosition - Variable in class etomica.modules.sam.P1WCAWall
-
- wallPotential - Variable in class etomica.modules.pistoncylinder.DataSourceWallPressure
-
- wallPotential - Variable in class etomica.modules.pistoncylinder.PistonCylinder
-
- wallPotential - Variable in class etomica.modules.sam.PotentialCalculationForceSumWall
-
- wallPotential - Variable in class etomica.modules.sam.Sam
-
- wallPotential - Variable in class etomica.modules.sam.WallPlane
-
- WallRangeModifier(P1Wall, CriterionPositionWall) - Constructor for class etomica.modules.colloid.ColloidGraphic.WallRangeModifier
-
- wallSpecies - Variable in class etomica.interfacial.MeterWallPosition
-
- warn(String) - Method in class org.jmol.util.DefaultLogger
-
- warn(String) - Static method in class org.jmol.util.Logger
-
Writes a log at WARN level.
- warn(String) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at WARN level.
- warnEx(String, Throwable) - Method in class org.jmol.util.DefaultLogger
-
- warnEx(String, Throwable) - Static method in class org.jmol.util.Logger
-
Writes a log at WARN level with detail on exception.
- warnEx(String, Throwable) - Method in interface org.jmol.util.LoggerInterface
-
Writes a log at WARN level with detail on exception.
- warningPrinted - Variable in class etomica.potential.PotentialCalculationPressureTensor
-
- WaterBox - Class in etomica.rotation
-
- WaterBox() - Constructor for class etomica.rotation.WaterBox
-
- WaterBox.Applet - Class in etomica.rotation
-
- WaterDroplet - Class in etomica.rotation
-
- WaterDroplet() - Constructor for class etomica.rotation.WaterDroplet
-
- WaterDroplet.Applet - Class in etomica.rotation
-
- WaterDropletMatrix - Class in etomica.rotation
-
- WaterDropletMatrix() - Constructor for class etomica.rotation.WaterDropletMatrix
-
- WaterDropletMatrix.Applet - Class in etomica.rotation
-
- WaterDropletRattle - Class in etomica.rotation
-
- WaterDropletRattle() - Constructor for class etomica.rotation.WaterDropletRattle
-
- WaterDropletRattle.Applet - Class in etomica.rotation
-
- WaterDropletShake - Class in etomica.rotation
-
- WaterDropletShake() - Constructor for class etomica.rotation.WaterDropletShake
-
- WaterDropletShake.Applet - Class in etomica.rotation
-
- WaterTrimer - Class in etomica.rotation
-
- WaterTrimer() - Constructor for class etomica.rotation.WaterTrimer
-
- WaterTrimer.Applet - Class in etomica.rotation
-
- WaterTrimerRattle - Class in etomica.rotation
-
- WaterTrimerRattle() - Constructor for class etomica.rotation.WaterTrimerRattle
-
- WaterTrimerRattle.Applet - Class in etomica.rotation
-
- WaterTrimerShake - Class in etomica.rotation
-
- WaterTrimerShake() - Constructor for class etomica.rotation.WaterTrimerShake
-
- WaterTrimerShake.Applet - Class in etomica.rotation
-
- Watt - Class in etomica.units
-
The Watt unit of power, equal to 1 J/s or 1 kg-m^2/s^3.
- Wavenumber - Class in etomica.units.dimensions
-
Dimension for all units of spatial frequency, 1/Length.
- waveVec - Variable in class etomica.data.meter.MeterStructureFactor
-
- waveVector - Variable in class etomica.normalmode.MeterHarmonicCoordinate
-
- waveVectorAction - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1DGraphic
-
- waveVectorCoefficients - Variable in class etomica.normalmode.CalcJacobian
-
- waveVectorCoefficients - Variable in class etomica.normalmode.MeterHarmonicEnergy
-
- waveVectorCoefficients - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- waveVectorFactory - Variable in class etomica.normalmode.NormalModeAnalysisDisplay1D
-
- waveVectorFactory - Variable in class etomica.normalmode.NormalModeAnalysisDisplay2D
-
- waveVectorFactory - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3D
-
- waveVectorFactory - Variable in class etomica.normalmode.NormalModes2D
-
- waveVectorFactory - Variable in class etomica.normalmode.NormalModes3D
-
- WaveVectorFactory - Interface in etomica.normalmode
-
Interface for a class the returns the appropriate wave vectors for a box
and primitive
- waveVectorFactory - Variable in class etomica.normalmode.WriteS
-
- WaveVectorFactory1D - Class in etomica.normalmode
-
Wave vector factory that returns wave vectors for a 1D system.
- WaveVectorFactory1D() - Constructor for class etomica.normalmode.WaveVectorFactory1D
-
- WaveVectorFactory2D - Class in etomica.normalmode
-
Wave vector factory that returns wave vectors appropriate for a box with
a single-atom basis.
- WaveVectorFactory2D(Primitive, Space) - Constructor for class etomica.normalmode.WaveVectorFactory2D
-
- WaveVectorFactoryFcc - Class in etomica.normalmode
-
WaveVectorFactory implementation that returns wave vectors appropriate for
a cubic FCC lattice.
- WaveVectorFactoryFcc(PrimitiveFcc, int) - Constructor for class etomica.normalmode.WaveVectorFactoryFcc
-
- WaveVectorFactoryFromFile - Class in etomica.normalmode
-
Obtains wave vectors and coefficients from a file.
- WaveVectorFactoryFromFile(String, int) - Constructor for class etomica.normalmode.WaveVectorFactoryFromFile
-
- WaveVectorFactorySimple - Class in etomica.normalmode
-
Wave vector factory that returns wave vectors appropriate for a box with
a single-atom basis.
- WaveVectorFactorySimple(Primitive, Space) - Constructor for class etomica.normalmode.WaveVectorFactorySimple
-
- WaveVectorFactorySuperBox - Class in etomica.normalmode
-
- WaveVectorFactorySuperBox(Primitive, Space) - Constructor for class etomica.normalmode.WaveVectorFactorySuperBox
-
- waveVectorMethod - Variable in class etomica.models.clathrates.ClathrateHarmonicFE.SimParams
-
- waveVectorMethod - Variable in class etomica.normalmode.NormalModesMolecular
-
- waveVectorNum - Variable in class etomica.normalmode.IntegratorHarmonic
-
- waveVectorPostAction - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- waveVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- waveVectors - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- waveVectors - Variable in class etomica.modules.sam.P1Sinusoidal
-
- waveVectors - Variable in class etomica.normalmode.CalcJacobian
-
- waveVectors - Variable in class etomica.normalmode.MeterHarmonicEnergy
-
- waveVectors - Variable in class etomica.normalmode.MeterHarmonicSingleEnergy
-
- waveVectors - Variable in class etomica.normalmode.NormalModesVariable
-
- waveVectors - Variable in class etomica.normalmode.WaveVectorFactory1D
-
- waveVectors - Variable in class etomica.normalmode.WaveVectorFactory2D
-
- waveVectors - Variable in class etomica.normalmode.WaveVectorFactoryFcc
-
- waveVectors - Variable in class etomica.normalmode.WaveVectorFactorySimple
-
- wavevectorx - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- wavevectory - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- wavevectorz - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
- wB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonic.SimOverlapParam
-
- wB - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
-
- weight - Variable in class etomica.tmmc.IntegratorTMMC
-
- weight - Variable in class etomica.virial.MeterVirialBDBin
-
- weight - Variable in class etomica.virial.MeterVirialBDBinMultiThreaded.MyData
-
- weight - Variable in class etomica.virial.MeterVirialBinMultiThreaded.MyData
-
- weight - Variable in class etomica.virial.MeterVirialEBinMultiThreaded.MyData
-
- weight - Variable in class etomica.virial.simulations.VirialH2OGCPMD.Clusterfoo
-
- weightCluster - Variable in class etomica.virial.ClusterWeightAbs
-
- weightNew - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- weightNew - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- weightNew - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- weightNew - Variable in class etomica.virial.MCMoveClusterRingScale
-
- weightOld - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- weightOld - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- weightOld - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- weightOld - Variable in class etomica.virial.MCMoveClusterRingScale
-
- weightSum - Variable in class etomica.data.histogram.HistogramReweightedData
-
- well2 - Variable in class etomica.virial.MayerWell
-
- wellConstant - Variable in class etomica.association.TestIGAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.association.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.association.TestLJAssociationMC3D_NPT_DoubleSites.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.association.TestLJAssociationMC3D_NVTOld.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid3Pt.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.virial.simulations.DoubleAssociationSitesFluid4Pt.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.virial.simulations.FourAssociationSitesFluid2Pt.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid2Pt.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid3Pt.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.virial.simulations.SingleAssociationSiteFluid4Pt.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.virial.simulations.TestLJAssociationMC3D_NPT.VirialAssociatingFluidParam
-
- wellConstant - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
-
- wellConstant - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
-
- wellDiameter - Variable in class etomica.modules.catalysis.P2SquareWellBonding
-
- wellDiameter - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- wellDiameter - Variable in class etomica.modules.catalysis.P2SquareWellSurface
-
- wellDiameter - Variable in class etomica.modules.mu.P2SquareWellOneSide
-
- wellDiameter - Variable in class etomica.potential.P2DoubleWell
-
- wellDiameter - Variable in class etomica.potential.P2SquareWell
-
- wellDiameter - Variable in class etomica.potential.P2SquareWellRobust
-
- wellDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellBonding
-
- wellDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellBondingCO
-
- wellDiameterSquared - Variable in class etomica.modules.catalysis.P2SquareWellSurface
-
- wellDiameterSquared - Variable in class etomica.modules.mu.P2SquareWellOneSide
-
- wellDiameterSquared - Variable in class etomica.potential.P2DoubleWell
-
- wellDiameterSquared - Variable in class etomica.potential.P2PenetrableSquareWell
-
- wellDiameterSquared - Variable in class etomica.potential.P2SquareWell
-
- wellDiameterSquared - Variable in class etomica.potential.P2SquareWellRobust
-
- wellManager - Variable in class etomica.potential.P2SquareWellRobust
-
- Wertheim2SiteAceticAcid - Class in etomica.association.AceticAcid
-
Wertheim coefficients calculation for acetic acid using IMPROVED OPLS united-atom model.
- Wertheim2SiteAceticAcid() - Constructor for class etomica.association.AceticAcid.Wertheim2SiteAceticAcid
-
- Wertheim2SiteAceticAcid.WertheimParam - Class in etomica.association.AceticAcid
-
Inner class for parameters
- WertheimAssociatingFluidParam() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam
-
- WertheimDiagrams2SiteRho - Class in etomica.virial.cluster
-
Wertheim diagram generator for 2 site model
- WertheimDiagrams2SiteRho(int, boolean, boolean, int, boolean) - Constructor for class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- WertheimDiagrams2SiteRho(int, boolean, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.WertheimDiagrams2SiteRho
-
- WertheimDiagrams3SiteRho - Class in etomica.virial.cluster
-
Wertheim diagram generator for GCPM water (3 site model)
- WertheimDiagrams3SiteRho(int, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- WertheimDiagrams3SiteRho(int, boolean, boolean, boolean, boolean) - Constructor for class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- WertheimGCPM3PtEBondDecomp - Class in etomica.association.GCPMWater
-
repulsive potential: energy of pair is greater than -3000cal/mol
attractive potential: energy of pair is less than -3000cal/mol
Wertheim's single attraction-site model of GCPM
Three Site model
e-bond in 3 body term is decomposed into eR and F
- WertheimGCPM3PtEBondDecomp() - Constructor for class etomica.association.GCPMWater.WertheimGCPM3PtEBondDecomp
-
- WertheimGCPM3PtEBondDecomp.VirialAssociatingFluidParam - Class in etomica.association.GCPMWater
-
- WertheimGCPM3PtThreeSite - Class in etomica.association.GCPMWater
-
repulsive potential: energy of pair is greater than -association energy(cal/mol)
attractive potential: energy of pair is less than -association energy(cal/mol)
Wertheim's three attraction-site model of GCPM
Three point diagram
Three Site model
- WertheimGCPM3PtThreeSite() - Constructor for class etomica.association.GCPMWater.WertheimGCPM3PtThreeSite
-
- WertheimGCPM3PtThreeSite.VirialAssociatingFluidParam - Class in etomica.association.GCPMWater
-
- WertheimGCPM4PtEBondDecomp - Class in etomica.association.GCPMWater
-
repulsive potential: energy of pair is greater than -2500cal/mol
attractive potential: energy of pair is less than -2500cal/mol
Wertheim's single attraction-site model of GCPM
Three Site model
e-bond in 4 body term is decomposed into eR and F
final revision Aug 2011
- WertheimGCPM4PtEBondDecomp() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecomp
-
- WertheimGCPM4PtEBondDecomp.WertheimAssociatingFluidParam - Class in etomica.association.GCPMWater
-
- WertheimGCPM4PtEBondDecompFinal - Class in etomica.association.GCPMWater
-
repulsive potential: energy of pair is greater than -3000cal/mol
attractive potential: energy of pair is less than -3000cal/mol
Wertheim's single attraction-site model of GCPM
Three Site model
e-bond in 4 body term is decomposed into eR and F
Flipping is applied in 28E calculation
final revision Aug 2011
- WertheimGCPM4PtEBondDecompFinal() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtEBondDecompFinal
-
- WertheimGCPM4PtEBondDecompFinal.VirialAssociatingFluidParam - Class in etomica.association.GCPMWater
-
- WertheimGCPM4PtThreeSite - Class in etomica.association.GCPMWater
-
repulsive potential: energy of pair is greater than -association E(cal/mol)
attractive potential: energy of pair is less than -association E(cal/mol)
Wertheim's three attraction-site model of GCPM
4th order diagram
last revision Aug 2011
- WertheimGCPM4PtThreeSite() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtThreeSite
-
- WertheimGCPM4PtThreeSite.VirialAssociatingFluidParam - Class in etomica.association.GCPMWater
-
- WertheimGCPM4PtThreeSiteEDecompDirectSampling - Class in etomica.association.GCPMWater
-
repulsive potential: energy of pair is greater than -association E(cal/mol)
attractive potential: energy of pair is less than -association E(cal/mol)
Wertheim's three attraction-site model of GCPM
Direct Sampling
Non-additive 4th order diagram
- WertheimGCPM4PtThreeSiteEDecompDirectSampling() - Constructor for class etomica.association.GCPMWater.WertheimGCPM4PtThreeSiteEDecompDirectSampling
-
- WertheimGCPM4PtThreeSiteEDecompDirectSampling.VirialAssociatingFluidParam - Class in etomica.association.GCPMWater
-
- WertheimParam() - Constructor for class etomica.association.AceticAcid.Wertheim2SiteAceticAcid.WertheimParam
-
- which - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceAlphaFE
-
- whichGraph - Variable in class etomica.virial.simulations.SingleAssociationSiteFluidGraph.VirialAssociatingFluidParam
-
- WHITE - Static variable in class org.jmol.util.Colix
-
- widom2Plot - Variable in class etomica.modules.insertion.InsertionGraphic
-
- widomHistPlot - Variable in class etomica.modules.insertion.InsertionGraphic
-
- width - Variable in class etomica.graph.view.rasterizer.SVGConverter
-
Output image width.
- width - Variable in class org.jmol.util.GData
-
- Wigner3j - Class in etomica.veos.bigdecimal
-
Exact representations of Wigner 3jm and 3nj values of half-integer arguments.
- Wigner3j() - Constructor for class etomica.veos.bigdecimal.Wigner3j
-
- wigner3j(String, String, String, String) - Static method in class etomica.veos.bigdecimal.Wigner3j
-
Wigner 3jn symbol.
- Wigner3jGUI - Class in etomica.veos.bigdecimal
-
An interactive interface to the Wigner3j class.
- Wigner3jGUI() - Constructor for class etomica.veos.bigdecimal.Wigner3jGUI
-
- wigner3jm(int, int, int, int, int, int) - Static method in class etomica.veos.bigdecimal.Wigner3j
-
The Wigner 3jm symbol (j1,j2,j3,m1,m2,m3).
- wigner3jm(Rational, Rational, Rational, Rational, Rational, Rational) - Static method in class etomica.veos.bigdecimal.Wigner3j
-
The Wigner 3jm symbol (j1,j2,j3,m1,m2,m3).
- wignerSeitzCell() - Method in class etomica.lattice.crystal.Primitive
-
Returns the Wigner-Seitz cell specified by this primitive.
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveBcc
-
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveCubic
-
Returns a new Square (if primitive is 2D) or Cube (if 3D) with edges
given by the size of the primitive vectors.
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveFcc
-
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveGeneral
-
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveHexagonal
-
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveHexagonal2D
-
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveMonoclinic
-
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombic
-
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveOrthorhombicHexagonal
-
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveTetragonal
-
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveTriclinic
-
- wignerSeitzCell() - Method in class etomica.lattice.crystal.PrimitiveTrigonal
-
- wignerSeitzCell() - Method in class etomica.models.hexane.PrimitiveHexane
-
- willDiscardNextData() - Method in class etomica.data.history.HistoryCollapsingDiscard
-
- willDiscardNextData() - Method in class etomica.data.history.HistoryComplete
-
- willDiscardNextData() - Method in class etomica.data.history.HistoryScrolling
-
- WINDOW_CLOSER - Static variable in class etomica.graphics.SimulationGraphic
-
- windowcentered - Static variable in class org.jmol.script.Token
-
- windowClosed(WindowEvent) - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
-
- windowClosing(WindowEvent) - Method in class etomica.virial.GUI.views.ViewConsoleOutputBox
-
- windowHeight - Variable in class org.jmol.util.GData
-
- windowWidth - Variable in class org.jmol.util.GData
-
- WIREFRAME - Static variable in class g3dsys.images.Bond
-
- wireframe - Static variable in class org.jmol.script.Token
-
- wireframerotation - Static variable in class org.jmol.script.Token
-
- within - Static variable in class org.jmol.script.Token
-
- withReplacement - Variable in class etomica.data.AccumulatorAverageBootstrap
-
- withReplacement - Variable in class etomica.data.AccumulatorAverageCollapsingLog
-
- wNew - Variable in class etomica.models.hexane.MCMoveCBMC
-
- wNew - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- wNew - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- wNew - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- wNew - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- wNew - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- wNew - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- wNew - Variable in class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- wNew - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- wNew - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- wNew - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- wNew - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- wNew - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- wOld - Variable in class etomica.models.hexane.MCMoveCBMC
-
- wOld - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- wOld - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- wOld - Variable in class etomica.virial.MCMoveClusterRingPartialRegrow
-
- wOld - Variable in class etomica.virial.MCMoveClusterRingRegrow
-
- wOld - Variable in class etomica.virial.MCMoveClusterRingRegrowExchange
-
- wOld - Variable in class etomica.virial.MCMoveClusterRotateCH3
-
- wOld - Variable in class etomica.virial.MCMoveClusterTorsionAceticAcid
-
- wOld - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- wOld - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- wOld - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- wOld - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- wOld - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- work - Variable in class etomica.data.AccumulatorAverageBlockless
-
- work - Variable in class etomica.data.AccumulatorAverageBlocklessSlim
-
- work - Variable in class etomica.data.AccumulatorAverageFixed
-
- work - Variable in class etomica.data.AccumulatorAverageFixedOutputFile
-
- work - Variable in class etomica.data.DataSourceTensorVirialHard
-
- work - Variable in class etomica.data.meter.MeterDipoleSumSquaredMappedAverage
-
- work - Variable in class etomica.models.co2.PNCO2GCPM
-
- work - Variable in class etomica.models.co2.PNGCPM
-
- work - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- work - Variable in class etomica.models.nitrogen.P2NitrogenAB
-
- work - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- work - Variable in class etomica.models.nitrogen.P2NitrogenShellModel
-
- work - Variable in class etomica.models.water.P2Water3P
-
- work - Variable in class etomica.models.water.P2Water4P
-
- work - Variable in class etomica.models.water.PNWaterGCPM
-
- work - Variable in class etomica.modules.droplet.AtomFilterLiquid
-
- work - Variable in class etomica.modules.rosmosis.P1Tether
-
- work - Variable in class etomica.normalmode.MeterDDP
-
- work - Variable in class etomica.normalmode.MeterDP
-
- work - Variable in class etomica.potential.P2CO2EMP
-
- work - Variable in class etomica.space3d.RotationTensor3D
-
- work1 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- work1 - Variable in class etomica.association.BiasVolumeAceticAcid
-
- work1 - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- work1 - Variable in class etomica.normalmode.CoordinateDefinitionMolecule
-
- work1 - Variable in class etomica.normalmode.CoordinateDefinitionMoleculeVolumeFluctuation
-
- work1 - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- work1 - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- work1 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- work1 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- work1 - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- work1 - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- work1 - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- work2 - Variable in class etomica.association.BiasVolume2SiteAceticAcid
-
- work2 - Variable in class etomica.association.BiasVolumeAceticAcid
-
- work2 - Variable in class etomica.data.AccumulatorAverageFixed
-
- work2 - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- work2 - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- work2 - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- work2 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- work2 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- work2 - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- work2 - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- work2 - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- work3 - Variable in class etomica.integrator.mcmove.MCMoveWiggleAceticAcid
-
- work3 - Variable in class etomica.virial.MCMoveClusterAngleBend
-
- work3 - Variable in class etomica.virial.MCMoveClusterAngleBendAceticAcid
-
- work3 - Variable in class etomica.virial.MCMoveClusterTorsionAlkaneEH
-
- work3 - Variable in class etomica.virial.MCMoveClusterTorsionMulti
-
- work3 - Variable in class etomica.virial.MCMoveClusterWiggleAceticAcid
-
- work3 - Variable in class etomica.virial.MCMoveClusterWiggleAlkaneEH
-
- work3 - Variable in class etomica.virial.MCMoveClusterWiggleMulti
-
- workArray - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- workArray - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- workAveCosTheta - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DN2AveCosThetaConstraint
-
- workdTorq - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- workTensor - Variable in class etomica.integrator.IntegratorRigidIterative
-
- workTensor - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- workTensor - Variable in class etomica.integrator.IntegratorVelocityVerlet
-
- workTensor - Variable in class etomica.integrator.IntegratorVerlet
-
- workTensor - Variable in class etomica.models.water.OrientationCalcWater3P
-
- workTensor - Variable in class etomica.models.water.OrientationCalcWater4P
-
- workTensor - Variable in class etomica.modules.droplet.IntegratorDroplet
-
- workTensor - Variable in class etomica.modules.droplet.MeterDeformation
-
- workTensor - Variable in class etomica.potential.PotentialCalculationPressureTensor
-
- workTensor - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- workTensor2 - Variable in class etomica.modules.droplet.IntegratorDroplet
-
- workTorqVec - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- workVec - Variable in class etomica.models.nitrogen.CalcAnalytical2ndDerivativeNitrogen
-
- workVec - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- workVec - Variable in class etomica.models.nitrogen.P2Nitrogen
-
- workVector - Variable in class etomica.dimer.IntegratorDimerMin
-
- workVector - Variable in class etomica.dimer.IntegratorDimerRT
-
- workVector - Variable in class etomica.models.nitrogen.MCMoveRotateMolecule3DConstraint
-
- workVector - Variable in class etomica.normalmode.CoordinateDefinitionLeaf
-
- workVector - Variable in class etomica.normalmode.MeterAtomicDisplacement
-
- workVector3 - Variable in class etomica.dimer.IntegratorDimerRT
-
- wrapped - Variable in class etomica.meta.wrappers.Wrapper
-
- wrappedClass - Variable in class etomica.meta.wrappers.Wrapper
-
- wrappedCluster - Variable in class etomica.virial.ClusterCoupledFlipped
-
- wrappedCluster - Variable in class etomica.virial.ClusterCoupledFlippedMultivalue
-
- wrappedDataSource - Variable in class etomica.data.meter.MeterPressureByVolumeChange.DataSourceExp
-
- wrappedId - Variable in class etomica.meta.wrappers.Wrapper
-
- wrappedPotential - Variable in class etomica.normalmode.P2XOrder
-
- wrappedPotential - Variable in class etomica.potential.P2HardWrapper
-
- wrappedPotential - Variable in class etomica.potential.P2MoleculeMonatomic
-
- wrappedPotential - Variable in class etomica.potential.P2SoftTruncated
-
- wrappedPotentialMaster - Variable in class etomica.normalmode.SimOverlapLJModule.APIPotentialTarget
-
- Wrapper<T> - Class in etomica.meta.wrappers
-
Surrogate for an instance of an object that is part of a simulation, providing greater control over which
fields are made accessible in the simulation model.
- Wrapper(T, SimulationModel, boolean) - Constructor for class etomica.meta.wrappers.Wrapper
-
- wrapper - Variable in class etomica.util.ParseArgs
-
- wrapper - Variable in class etomica.util.ReadParameters
-
- wrapper - Variable in class etomica.util.WriteParameters
-
- WrapperIndex - Class in etomica.meta
-
Provides a map between a class and the constructor of its appropriate wrapper type.
- WrapperIndex() - Constructor for class etomica.meta.WrapperIndex
-
- WrapperSerializer - Class in etomica.server.serializers
-
- WrapperSerializer() - Constructor for class etomica.server.serializers.WrapperSerializer
-
- wRatio - Variable in class etomica.virial.MCMoveClusterRingScale
-
- write(Exception) - Method in interface etomica.graph.engine.Console
-
- write(String) - Method in interface etomica.graph.engine.Console
-
- write(Exception) - Method in class etomica.graph.engine.ConsoleUI
-
- write(String) - Method in class etomica.graph.engine.ConsoleUI
-
- write(Parser.CommandVariableValue) - Method in class etomica.graph.engine.Interpreter
-
- writeAtom(FileWriter, IAtom) - Method in class etomica.action.WriteConfiguration
-
- writeAtom(FileWriter, IAtom) - Method in class etomica.action.WriteConfigurationOriented
-
- writeAtom(FileWriter, IAtom) - Method in class etomica.interfacial.WriteConfigurationInterfacial
-
- WriteConfiguration - Class in etomica.action
-
Dumps a box's configuration to a file.
- WriteConfiguration(Space) - Constructor for class etomica.action.WriteConfiguration
-
- writeConfiguration(String) - Method in class etomica.kmc.IntegratorKMC
-
- writeConfiguration(String) - Method in class etomica.kmc.IntegratorKMCCluster
-
- writeConfiguration(String) - Method in class etomica.models.nitrogen.SimDirectBetaN2RPAngleToNoAngle
-
- writeConfiguration(String) - Method in class etomica.models.nitrogen.SimDirectBetaN2RPInitPert
-
- writeConfiguration(String) - Method in class etomica.models.nitrogen.SimDirectDisorderedAlphaN2RPInitPert
-
- writeConfiguration(String) - Method in class etomica.models.nitrogen.SimOverlapAlphaN2TP
-
- writeConfiguration(String) - Method in class etomica.models.nitrogen.SimOverlapBetaN2RPScaling
-
- writeConfiguration(String) - Method in class etomica.models.nitrogen.SimOverlapBetaN2TP
-
- writeConfiguration(String) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2RPScaling
-
- writeConfiguration(String) - Method in class etomica.models.nitrogen.SimOverlapDisorderedAlphaN2TP
-
- writeConfiguration(String) - Method in class etomica.normalmode.SimFluidSoftSphere
-
- WriteConfigurationBinary - Class in etomica.action
-
Dumps a box's configuration to a file.
- WriteConfigurationBinary(Space) - Constructor for class etomica.action.WriteConfigurationBinary
-
- WriteConfigurationDLPOLY - Class in etomica.action
-
Dumps a box's configuration to a file.
- WriteConfigurationDLPOLY() - Constructor for class etomica.action.WriteConfigurationDLPOLY
-
- WriteConfigurationInterfacial - Class in etomica.interfacial
-
Dumps a box's configuration to a file.
- WriteConfigurationInterfacial(Space) - Constructor for class etomica.interfacial.WriteConfigurationInterfacial
-
- WriteConfigurationOriented - Class in etomica.action
-
WriteConfiguration subclass capable of handling oriented atoms.
- WriteConfigurationOriented(Space) - Constructor for class etomica.action.WriteConfigurationOriented
-
- WriteConfigurationP2DLPOLY - Class in etomica.action
-
Dumps a box's configuration to a file.
- WriteConfigurationP2DLPOLY() - Constructor for class etomica.action.WriteConfigurationP2DLPOLY
-
- writeD(AkimaSplineSmoother, String, int) - Static method in class etomica.math.numerical.AkimaSplineSmootherMain
-
- writeData() - Method in interface etomica.threaded.IPotentialCalculationThreaded
-
- writeData() - Method in class etomica.threaded.PotentialCalculationForceSumThreaded
-
- writeData() - Method in class etomica.threads.ThreadsMD
-
- writeData(String) - Method in class etomica.virial.MeterVirialBDBin
-
- writeData(String) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- writeData(String, Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>, long) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- writeData(String) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- writeData(String, Map<IntSet, MeterVirialBinMultiThreaded.MyData>, long) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
-
- writeData(String) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- writeData(String, Map<IntSet, MeterVirialEBinMultiThreaded.MyData>, long, int) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- writeDataToFile(String) - Method in class etomica.action.CalcVibrationalModes
-
- writedb(Parser.CommandValue) - Method in class etomica.graph.engine.Interpreter
-
- writeDiagrams() - Method in class etomica.virial.cluster.ClusterDiagramTree
-
- writeFile(MeterStructureFactor, double, int) - Static method in class etomica.freeenergy.npath.ConfigFromFileLAMMPS
-
- WriteHistograms - Class in etomica.models.oneDHardRods
-
- WriteHistograms() - Constructor for class etomica.models.oneDHardRods.WriteHistograms
-
- WriteHistograms(String) - Constructor for class etomica.models.oneDHardRods.WriteHistograms
-
- writeLn() - Method in interface etomica.graph.engine.Console
-
- writeLn() - Method in class etomica.graph.engine.ConsoleUI
-
- writeMethod - Variable in class etomica.modifier.ModifierGeneral
-
- WriteParameters - Class in etomica.util
-
This class writes input parameters from a parameter wrapper Object to a file.
- WriteParameters() - Constructor for class etomica.util.WriteParameters
-
- WriteParameters(String) - Constructor for class etomica.util.WriteParameters
-
- WriteParameters(String, ParameterBase) - Constructor for class etomica.util.WriteParameters
-
- writeParameters() - Method in class etomica.util.WriteParameters
-
Reads each line from inputFileName and attempts to match it with a field
from parameterWrapper and sets the field to the value from the file.
- writePosition - Variable in class etomica.action.WriteConfiguration
-
- writePosition - Variable in class etomica.action.WriteConfigurationBinary
-
- writer - Variable in class etomica.dimer.IntegratorDimerMin
-
- writeRasmolScript(DiameterHashByType) - Method in class etomica.action.PDBWriter
-
Writes a script for rasmol that initializes the radii of each atom type.
- writeRasmolScript(DiameterHashByType) - Method in class etomica.action.XYZWriter
-
Writes a script for rasmol that initializes the radii of each atom type.
- writeRefPref - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditive.VirialParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical.VirialParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialCPSHeliumNonAdditiveClassical_Correction.VirialParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialHardAssociationCone.VirialLJParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialHardAssociationConeDoubleSites.VirialLJParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialHePCKLJS.VirialParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialHePCKLJSCHNCCorrection.VirialLJParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialHePCKLJSPYCorrection.VirialLJParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialHePCKLJSTempDeriv.VirialParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialLJ.VirialLJParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialLJCHNCCorrection.VirialLJParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialLJD.VirialLJParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialLJPYCorrection.VirialLJParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialLJSeries.VirialLJParam
-
- writeRefPref - Variable in class etomica.virial.simulations.VirialSW.VirialSWParam
-
- WriteS - Class in etomica.normalmode
-
Class that writes out S from the MeterNormalMode, calculates
eigenvectors/values (writes them out) and calculates the harmonic free
energy from them.
- WriteS(Space) - Constructor for class etomica.normalmode.WriteS
-
- writeSetToFile(Set<Graph>, String) - Static method in class etomica.virial.cluster.WertheimDiagrams3SiteRho
-
- writeUdistribution(String) - Method in class etomica.models.nitrogen.MeterNormalizedCoordBeta
-
- writeUdistribution(String) - Method in class etomica.models.nitrogen.MeterOrientationDistribution
-
- writeUdistribution(String) - Method in class etomica.models.nitrogen.MeterRotationDistributionGroup
-
- writeWeights(String) - Method in class etomica.virial.MeterVirialBDBin
-
- writeWeights(String) - Method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- writeWeights(String, Map<IntSet, MeterVirialBDBinMultiThreaded.MyData>) - Static method in class etomica.virial.MeterVirialBDBinMultiThreaded
-
- writeWeights(String) - Method in class etomica.virial.MeterVirialBinMultiThreaded
-
- writeWeights(String, Map<IntSet, MeterVirialBinMultiThreaded.MyData>) - Static method in class etomica.virial.MeterVirialBinMultiThreaded
-
- writeWeights(String) - Method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- writeWeights(String, Map<IntSet, MeterVirialEBinMultiThreaded.MyData>) - Static method in class etomica.virial.MeterVirialEBinMultiThreaded
-
- wvCoeff - Variable in class etomica.models.oneDHardRods.MeterDifferentImageAdd
-
- wvCoeff - Variable in class etomica.models.oneDHardRods.MeterDifferentImageSubtract
-
- wvTable - Variable in class etomica.normalmode.NormalModeAnalysisDisplay3DGraphic
-
X
- X - Variable in class etomica.conjugategradient.ConjugateGradients
-
- X - Variable in class etomica.conjugategradient.PreconditionedConjugateGradient
-
- X - Variable in class etomica.conjugategradient.SteepestDescent
-
- x - Variable in class etomica.data.types.DataDouble
-
The wrapped data value held by this object.
- x - Variable in class etomica.data.types.DataTensor
-
The wrapped tensor data.
- x - Variable in class etomica.data.types.DataVector
-
The wrapped vector data.
- x - Variable in class etomica.math.ErfcBenchmark
-
- x - Variable in class etomica.math.numerical.AkimaSpline
-
- x - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- x - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- x - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- x - Variable in class etomica.modules.statistics.DataProcessorBounds
-
- x - Variable in class etomica.nbr.CriterionPositionWall.DoubleWrapper
-
- x - Variable in class etomica.space3d.Vector3D
-
- x - Variable in class etomica.spaceNd.TensorND
-
- x - Variable in class etomica.spaceNd.VectorND
-
- x - Variable in class etomica.util.Grabber.CornerData
-
- x - Static variable in class org.jmol.script.Token
-
- x - Variable in class org.jmol.util.AxisAngle4f
-
The x coordinate.
- x - Variable in class org.jmol.util.Tuple3f
-
The x coordinate.
- x - Variable in class org.jmol.util.Tuple3i
-
The x coordinate.
- x - Variable in class org.jmol.util.Tuple4f
-
The x coordinate.
- x0 - Variable in class etomica.gaussianwork.SimOverlapMultiHarmonicOptRefPref.SimOverlapParam
-
- x0 - Variable in class etomica.mappedRdf.PotentialCalculationMappedRdf
-
- x0 - Variable in class etomica.mappedvirial.PotentialCalculationMappedEnergy
-
- x0 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirial
-
- x0 - Variable in class etomica.mappedvirial.PotentialCalculationMappedVirialV
-
- x0 - Variable in class etomica.normalmode.SimEinStep1.SimOverlapParam
-
- x0 - Variable in class etomica.normalmode.SimEinStep1HCP.SimOverlapParam
-
- x0 - Variable in class etomica.normalmode.SimEinStep2.SimOverlapParam
-
- x0 - Variable in class etomica.normalmode.SimEinStep2HCP.SimOverlapParam
-
- X_DIM - Static variable in class etomica.graphics.DevicePlotPoints
-
- xCell - Variable in class etomica.normalmode.ModifierYCells2D
-
- xd - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- xd - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- xData - Variable in class etomica.data.DataSourceRmsVelocity
-
- xData - Variable in class etomica.data.meter.MeterStructureFactor
-
- xData - Variable in class etomica.mappedvirial.MeterMeanForce
-
- xData - Variable in class etomica.modules.chainequilibrium.MeterChainLength
-
- xData - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- xData - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- xData - Variable in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- xData - Variable in class etomica.normalmode.DataSourceFE
-
- xData - Variable in class etomica.normalmode.DataSourceFEHistogram
-
- xData - Variable in class etomica.normalmode.DataSourceImposedFEFit
-
- xData - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
-
- xData - Variable in class etomica.normalmode.DataSourcePMu
-
- xData - Variable in class etomica.normalmode.DataSourcePN
-
- xData - Variable in class etomica.normalmode.MeterTiltHistogram
-
- xDataInfo - Variable in class etomica.data.DataSourceRmsVelocity
-
- xDataInfo - Variable in class etomica.data.meter.MeterStructureFactor
-
- xDataInfo - Variable in class etomica.mappedvirial.MeterMeanForce
-
- xDataInfo - Variable in class etomica.modules.chainequilibrium.MeterChainLength
-
- xDataInfo - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- xDataInfo - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- xDataInfo - Variable in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- xDataInfo - Variable in class etomica.normalmode.DataSourceFE
-
- xDataInfo - Variable in class etomica.normalmode.DataSourceFEHistogram
-
- xDataInfo - Variable in class etomica.normalmode.DataSourceImposedFEFit
-
- xDataInfo - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
-
- xDataInfo - Variable in class etomica.normalmode.DataSourcePMu
-
- xDataInfo - Variable in class etomica.normalmode.DataSourcePN
-
- xDataInfo - Variable in class etomica.normalmode.MeterTiltHistogram
-
- xDataSource - Variable in class etomica.data.AccumulatorHistogram
-
- xDataSource - Variable in class etomica.data.HistogramDataSource
-
- xDataSource - Variable in class etomica.data.meter.MeterDihedralAngle
-
- xDataSource - Variable in class etomica.data.meter.MeterProfileByAtoms
-
- xDataSource - Variable in class etomica.data.meter.MeterProfileByVolume
-
- xDataSource - Variable in class etomica.data.meter.MeterRDF
-
- xDataSource - Variable in class etomica.data.meter.MeterRDFPC
-
- xDataSource - Variable in class etomica.data.meter.PotentialCalculationRDF
-
- xDataSource - Variable in class etomica.data.types.DataFunction.DataInfoFunction
-
- xDataSource - Variable in class etomica.data.types.DataFunction.DataInfoFunctionFactory
-
- xDataSource - Variable in class etomica.gaussianwork.MeterWorkABandReweighting
-
- xDataSource - Variable in class etomica.gaussianwork.MeterWorkBAandReweighting
-
- xDataSource - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- xDataSource - Variable in class etomica.modules.adsorption.DataSourceDensityFunction
-
- xDataSource - Variable in class etomica.normalmode.MeterTiltRotationHistogram
-
- xDataSource - Variable in class etomica.normalmode.MeterWorkHarmonicTargetandReweighting
-
- xDataSource - Variable in class etomica.normalmode.MeterWorkTargetHarmonicandReweighting
-
- xDataSources - Variable in class etomica.data.AccumulatorHistory
-
- xDropAxis - Variable in class etomica.modules.droplet.DropletAtomic
-
- XE(Vector) - Method in interface etomica.space.Vector
-
Sets this vector equal to the cross product of this vector with the
given vector (only works for 3D vectors).
- XE(Vector) - Method in class etomica.space1d.Vector1D
-
- XE(Vector) - Method in class etomica.space2d.Vector2D
-
- XE(Vector) - Method in class etomica.space3d.Vector3D
-
- XE(Vector) - Method in class etomica.spaceNd.VectorND
-
- xGT - Static variable in class org.jmol.util.GData
-
- xInfo - Variable in class etomica.modules.statistics.DataProcessorBounds
-
- xIntercept() - Method in class etomica.math.geometry.Plane
-
Returns the intercept of the plane with the x-axis.
- xLabel - Variable in class etomica.graphics.DisplayPlot
-
- xLast - Variable in class org.jmol.util.GData
-
- xLat - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
-
- xlateDown() - Method in class g3dsys.control.G3DSys
-
Translate model 10% of pixel width down (+y)
- xlateLeft() - Method in class g3dsys.control.G3DSys
-
Translate model 10% of pixel width to the left (-x)
- xlateRight() - Method in class g3dsys.control.G3DSys
-
Translate model 10% of pixel width to the right (+x)
- xlateUp() - Method in class g3dsys.control.G3DSys
-
Translate model 10% of pixel width up (-y)
- xlateXY(int, int) - Method in class g3dsys.control.G3DSys
-
Trnaslate model x,y pixels
- xLight - Static variable in class org.jmol.util.Shader
-
- xlp - Static variable in class etomica.potential.P1HydrogenMielke
-
- xLT - Static variable in class org.jmol.util.GData
-
- xLxyz - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
-
- xMax - Variable in class etomica.data.histogram.HistogramNotSoSimple
-
- xMax - Variable in class etomica.data.histogram.HistogramReweightedData
-
- xMax - Variable in class etomica.data.histogram.HistogramSimple
-
- xMax - Variable in class etomica.data.meter.MeterRDF
-
- xMax - Variable in class etomica.data.meter.MeterRDFPC
-
- xMax - Variable in class etomica.data.meter.PotentialCalculationRDF
-
- xMax - Variable in class etomica.integrator.mcmove.MCMoveAtomInRegion
-
- xMax - Variable in class etomica.mappedRdf.MeterMappedRdf
-
- xMax - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- xMax - Variable in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
-
- xmax_ - Variable in class etomica.modules.clustergenerator.Plot
-
- xMaxp - Variable in class etomica.potential.P3HydrogenManzhos
-
- xMaxt - Variable in class etomica.potential.P3HydrogenManzhos
-
- xMin - Variable in class etomica.data.histogram.HistogramNotSoSimple
-
- xMin - Variable in class etomica.data.histogram.HistogramReweightedData
-
- xMin - Variable in class etomica.data.histogram.HistogramSimple
-
- xMin - Variable in class etomica.integrator.mcmove.MCMoveAtomInRegion
-
- xMin - Variable in class etomica.modules.adsorption.MeterExcessAdsorbed
-
- xMin - Variable in class etomica.modules.adsorption.MeterProfileByVolumeAdsorption
-
- xmin_ - Variable in class etomica.modules.clustergenerator.Plot
-
- xMinp - Variable in class etomica.potential.P3HydrogenManzhos
-
- xMint - Variable in class etomica.potential.P3HydrogenManzhos
-
- xNorm - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- xor(Bitmap) - Method in interface etomica.graph.model.Bitmap
-
Updates this bitmap with the result of the bitwise AND with the other bitmap: bitmap
= (bitmap ^ other).
- xor(Bitmap) - Method in class etomica.graph.model.impl.AbstractBitmap
-
- xor(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLong
-
TIME = O(1) for a compatible instance.
- xor(Bitmap) - Method in class etomica.graph.model.impl.BitmapOfLongVector
-
- xor(BitSet) - Method in class org.jmol.util.BitSet
-
Performs a logical XOR of this bit set with the bit set argument.
- xPixel(double) - Method in class etomica.modules.clustergenerator.Plot
-
Computes the x pixel value of a point in the world window.
- xPixels - Variable in class etomica.modules.clustergenerator.Plot
-
- xPos - Static variable in class etomica.potential.P2HydrogenPatkowski
-
- xPos - Static variable in class etomica.potential.P2HydrogenPatkowskiAtomic
-
- xPos - Variable in class etomica.potential.P3HydrogenManzhos
-
- xSlider - Variable in class etomica.modules.interfacial.InterfacialSWGraphic
-
- xTag - Variable in class etomica.data.DataSourceRmsVelocity
-
- xTag - Variable in class etomica.data.meter.MeterStructureFactor
-
- xTag - Variable in class etomica.mappedvirial.MeterMeanForce
-
- xTag - Variable in class etomica.modules.chainequilibrium.MeterChainLength
-
- xTag - Variable in class etomica.modules.interfacial.DataSourceTensorVirialHardProfile
-
- xTag - Variable in class etomica.modules.multiharmonic.overlap.MultiharmonicGraphicMC.DataSourceFunctionRaw
-
- xTag - Variable in class etomica.modules.statistics.StatisticsMCGraphic.DataProcessorUndo
-
- xTag - Variable in class etomica.normalmode.DataSourceFE
-
- xTag - Variable in class etomica.normalmode.DataSourceFEHistogram
-
- xTag - Variable in class etomica.normalmode.DataSourceImposedFEFit
-
- xTag - Variable in class etomica.normalmode.DataSourceImposedFEHistogram
-
- xTag - Variable in class etomica.normalmode.DataSourcePMu
-
- xTag - Variable in class etomica.normalmode.DataSourcePN
-
- xTag - Variable in class etomica.normalmode.MeterTiltHistogram
-
- xTriplePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- xType - Variable in class etomica.models.rowley.SpeciesEthanol
-
- xType - Variable in class etomica.models.rowley.SpeciesMethanol
-
- xValues() - Method in interface etomica.data.histogram.Histogram
-
Returns the x values from the histogram as an array of doubles
- xValues - Variable in class etomica.data.histogram.HistogramDiscrete
-
- xValues() - Method in class etomica.data.histogram.HistogramDiscrete
-
- xValues - Variable in class etomica.data.histogram.HistogramNotSoSimple
-
- xValues() - Method in class etomica.data.histogram.HistogramNotSoSimple
-
- xValues - Variable in class etomica.data.histogram.HistogramReweightedData
-
- xValues() - Method in class etomica.data.histogram.HistogramReweightedData
-
- xValues - Variable in class etomica.data.histogram.HistogramSimple
-
- xValues() - Method in class etomica.data.histogram.HistogramSimple
-
- xValues - Variable in class etomica.data.history.HistoryCollapsing
-
- xValues - Variable in class etomica.data.history.HistoryScrolling
-
- xVecBox - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- xVecBox - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- xVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- xVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- xVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- xVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- xVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- xVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- xVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- xVecBox - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- xveci - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- xveci - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- xvecj - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- xvecj - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- xveck - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- xveck - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- xWork - Variable in class etomica.integrator.IntegratorRigidIterative
-
- xWork - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- xWork - Variable in class etomica.models.water.OrientationCalcWater3P
-
- xWork - Variable in class etomica.models.water.OrientationCalcWater4P
-
- xWork - Variable in class etomica.rotation.IntegratorVelocityVerletQuaternion
-
- xx - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- xx - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- xx - Variable in class etomica.space3d.Tensor3D
-
- xy - Variable in class etomica.space3d.Tensor3D
-
- XY_ZTOP - Static variable in class org.jmol.viewer.JmolConstants
-
- xyz - Static variable in class org.jmol.script.Token
-
- XYZWriter - Class in etomica.action
-
Action that dumps a box's configuration to an XYZ file.
- XYZWriter(Box) - Constructor for class etomica.action.XYZWriter
-
- xz - Variable in class etomica.space3d.Tensor3D
-
- xz1 - Variable in class etomica.dimer.P1LepsHarmonic
-
- xz2 - Variable in class etomica.dimer.P1LepsHarmonic
-
- xzOrientationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- xzOrientationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- xzOrientationTensor - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
Y
- y - Variable in class etomica.data.meter.MeterProfileByAtoms
-
- y - Variable in class etomica.integrator.mcmove.MCMoveOverlapListener
-
- y - Variable in class etomica.liquidLJ.LjMd3Dv2y.LjMd3DParams
-
- y - Variable in class etomica.math.numerical.AkimaSpline
-
- y - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- y - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- y - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- Y - Variable in class etomica.math.numerical.PadeApproximation
-
- y - Variable in class etomica.potential.P3HydrogenManzhos
-
- y - Variable in class etomica.space3d.Vector3D
-
- y - Variable in class etomica.util.Grabber.CornerData
-
- y - Static variable in class org.jmol.script.Token
-
- y - Variable in class org.jmol.util.AxisAngle4f
-
The y coordinate.
- y - Variable in class org.jmol.util.Tuple3f
-
The y coordinate.
- y - Variable in class org.jmol.util.Tuple3i
-
The y coordinate.
- y - Variable in class org.jmol.util.Tuple4f
-
The y coordinate.
- y0 - Variable in class etomica.math.numerical.AkimaSplineSmoother
-
- y0 - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- y0 - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- Y_DIM - Static variable in class etomica.graphics.DevicePlotPoints
-
- yCell - Variable in class etomica.normalmode.ModifierXCells2D
-
- yDoublePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- YELLOW - Static variable in class org.jmol.util.Colix
-
- YesRemoveSpeciesButtonListener() - Constructor for class etomica.virial.GUI.controllers.ControllerAlertMsgBoxSpeciesRemoval.YesRemoveSpeciesButtonListener
-
- yGT - Static variable in class org.jmol.util.GData
-
- yIntercept() - Method in class etomica.math.geometry.Plane
-
Returns the intercept of the plane with the y-axis.
- yLast - Variable in class org.jmol.util.GData
-
- yLat - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
-
- yLight - Static variable in class org.jmol.util.Shader
-
- yLT - Static variable in class org.jmol.util.GData
-
- yLxyz - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
-
- ymax_ - Variable in class etomica.modules.clustergenerator.Plot
-
- ymin_ - Variable in class etomica.modules.clustergenerator.Plot
-
- yNorm - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- yOffset - Variable in class etomica.modules.catalysis.ConfigurationCatalysis
-
- yOffset - Variable in class etomica.modules.sam.ConfigurationSAM
-
- yOrientationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogen
-
- yOrientationTensor - Variable in class etomica.models.nitrogen.CoordinateDefinitionNitrogenSuperBox
-
- yOrientationTensor - Variable in class etomica.models.nitrogen.LatticeSumCrystalMolecular
-
- yPixel(double) - Method in class etomica.modules.clustergenerator.Plot
-
Computes the y pixel value of a point in the world window.
- yPixels - Variable in class etomica.modules.clustergenerator.Plot
-
- ySmooth - Variable in class etomica.math.numerical.AkimaSplineSmootherApp
-
- ySmooth - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- yTriplePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- yTrue - Variable in class etomica.math.numerical.AkimaSplineSmootherDyApp
-
- yVecBox - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- yVecBox - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- yVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- yVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- yVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- yVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- yVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- yVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- yVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- yVecBox - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- yveci - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- yveci - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- yvecj - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- yvecj - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- yveck - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- yveck - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- yWork - Variable in class etomica.integrator.IntegratorRigidMatrixIterative
-
- yWork - Variable in class etomica.models.water.OrientationCalcWater3P
-
- yWork - Variable in class etomica.models.water.OrientationCalcWater4P
-
- yx - Variable in class etomica.space3d.Tensor3D
-
- yy - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- yy - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- yy - Variable in class etomica.space3d.Tensor3D
-
- yz - Variable in class etomica.space3d.Tensor3D
-
- yz1 - Variable in class etomica.dimer.P1LepsHarmonic
-
- yz2 - Variable in class etomica.dimer.P1LepsHarmonic
-
Z
- Z - Variable in class etomica.math.numerical.PadeApproximation
-
- Z - Variable in class etomica.meam.ParameterSetMEAM
-
- Z - Variable in class etomica.potential.P3CPSNonAdditiveHeSimplified
-
- z - Variable in class etomica.space3d.Vector3D
-
- z - Static variable in class org.jmol.script.Token
-
- z - Variable in class org.jmol.util.AxisAngle4f
-
The z coordinate.
- z - Variable in class org.jmol.util.Tuple3f
-
The z coordinate.
- z - Variable in class org.jmol.util.Tuple3i
-
The z coordinate.
- z - Variable in class org.jmol.util.Tuple4f
-
The z coordinate.
- Z3 - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z3 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- Z3 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- Z3_111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z3_111 - Static variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- Z3_112 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z3_113 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z3_122 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z3_222 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z4211 - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z4211 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- Z4211 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- Z4211_1112 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z4211_1121 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z4211_2111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z4220 - Variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z4220 - Variable in class etomica.potential.P3CPSNonAdditiveHeLessSimplified
-
- Z4220 - Variable in class etomica.potential.P3CPSNonAdditiveHeOrig
-
- Z4220_1111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z4220_1211 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- Z4220_2111 - Static variable in class etomica.potential.P3CPSNonAdditiveHe
-
- zbuf - Variable in class org.jmol.g3d.Graphics3D
-
- zbufT - Variable in class org.jmol.g3d.Graphics3D
-
- zdepth - Static variable in class org.jmol.script.Token
-
- zDepth - Variable in class org.jmol.util.GData
-
- zDoublePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- Zeolite - Class in etomica.zeolite
-
- Zeolite() - Constructor for class etomica.zeolite.Zeolite
-
- zeoliteSimGraphic - Class in etomica.zeolite
-
- zeoliteSimGraphic(ZeoliteSimulation, Space) - Constructor for class etomica.zeolite.zeoliteSimGraphic
-
- zeoliteSimGraphic(ZeoliteSimulation, Space, String) - Constructor for class etomica.zeolite.zeoliteSimGraphic
-
- ZeoliteSimStart - Class in etomica.zeolite
-
- ZeoliteSimStart(ZeoliteSimulation, zeoliteSimGraphic) - Constructor for class etomica.zeolite.ZeoliteSimStart
-
- ZeoliteSimStart(IntegratorMD, boolean, int) - Constructor for class etomica.zeolite.ZeoliteSimStart
-
- ZeoliteSimulation - Class in etomica.zeolite
-
Three-dimensional hard-sphere molecular dynamics simulation, using
neighbor listing.
- ZERO - Static variable in class etomica.graph.model.BitmapFactory
-
- ZERO - Static variable in class etomica.math.Rational
-
- ZERO - Static variable in class etomica.veos.bigdecimal.BigSurd
-
The value of zero.
- ZERO - Static variable in class etomica.veos.bigdecimal.BigSurdVec
-
The value of zero.
- ZERO - Static variable in class etomica.veos.bigdecimal.Ifactor
-
- ZERO - Static variable in class etomica.veos.bigdecimal.Rational
-
The constant 0.
- ZERO - Static variable in class etomica.veos.BigValue
-
- zerobasedxyzrasmol - Static variable in class org.jmol.script.Token
-
- zeroF - Variable in class etomica.freeenergy.npath.P1ImageHarmonic
-
- zeros - Static variable in class etomica.data.types.DataDoubleBDArray
-
- zeroSum() - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergies
-
- zeroSum() - Method in class etomica.freeenergy.npath.DataSourceEnergies.PotentialCalculationEnergiesEAM
-
- zeroSum() - Method in class etomica.liquidLJ.PotentialCalculationEnergySumCutoff
-
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
- zeroSum() - Method in class etomica.meam.PotentialCalculationEnergySumEAM
-
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
- zeroSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuper
-
- zeroSum() - Method in class etomica.normalmode.PotentialCalculationSolidSuperCut
-
- zeroSum() - Method in class etomica.potential.PotentialCalculationEnergySum
-
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
- zeroSum() - Method in class etomica.potential.PotentialCalculationEnergySumBigDecimal
-
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
- zeroSum() - Method in class etomica.potential.PotentialCalculationHyperVirialSum
-
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
- zeroSum() - Method in class etomica.potential.PotentialCalculationMolecularVirialSum
-
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
- zeroSum() - Method in class etomica.potential.PotentialCalculationPhiSum
-
- zeroSum() - Method in class etomica.potential.PotentialCalculationPressureTensor
-
- zeroSum() - Method in class etomica.potential.PotentialCalculationVirialSum
-
Sets the virial sum to zero, typically to begin a new virial-sum calculation.
- zeroSums() - Method in class etomica.liquidLJ.PotentialCalculationSumCutoff
-
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
- zeroSums() - Method in class etomica.liquidLJ.PotentialCalculationSumCutoffLS
-
Sets the energy sum to zero, typically to begin a new energy-sum calculation.
- zeta(int, MathContext) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Riemann zeta function.
- zeta1(int) - Static method in class etomica.veos.bigdecimal.BigDecimalMath
-
Riemann zeta function.
- ZFcc(double, double) - Static method in class etomica.statmech.LennardJones
-
Compressibility factor, P/rho/kT for the fcc solid.
- zFluid(double) - Static method in class etomica.statmech.HardSphereFluid
-
Computes Z using the following equation
Z = exp([Ni * rho^(i-1)] + rho^11 [Mi x^i]) where x = a^rho
- zGT - Static variable in class org.jmol.util.GData
-
- zIntercept() - Method in class etomica.math.geometry.Plane
-
Returns the intercept of the plane with the z-axis.
- zk - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- zl - Variable in class etomica.models.nitrogen.P2NitrogenAnisotropic
-
- zLat - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
-
- zLight - Static variable in class org.jmol.util.Shader
-
- zLT - Static variable in class org.jmol.util.GData
-
- zLxyz - Variable in class etomica.liquidLJ.Potential2SoftSphericalLSMultiLatSlanty
-
- zMargin - Variable in class org.jmol.g3d.Graphics3D
-
- zMax - Variable in class etomica.interfacial.ConfigurationLammps
-
- zNorm - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- zoomDown(int) - Method in class g3dsys.control.G3DSys
-
Decrease the zoom level by i percent
- zoomenabled - Static variable in class org.jmol.script.Token
-
- zoomlarge - Static variable in class org.jmol.script.Token
-
- zoomUp(int) - Method in class g3dsys.control.G3DSys
-
Increase the zoom level by i percent
- zQuadruplePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- zshade - Static variable in class org.jmol.script.Token
-
- zShadeB - Variable in class org.jmol.util.GData
-
- zShadeG - Variable in class org.jmol.util.GData
-
- zshadepower - Static variable in class org.jmol.script.Token
-
- zShadePower - Variable in class org.jmol.util.GData
-
- zShadeR - Variable in class org.jmol.util.GData
-
- zShift - Variable in class etomica.interfacial.MeterWallPosition
-
- zslab - Static variable in class org.jmol.script.Token
-
- zSlab - Variable in class org.jmol.util.GData
-
- zSolid(double) - Method in class etomica.statmech.HardSphere
-
Returns the compressibility factor for solid (FCC) hard spheres at the
given density.
- zSolid(double) - Static method in class etomica.statmech.HardSphereSolid
-
Returns the compressibility factor for solid (FCC) hard spheres at the
given density.
- zSolidCorrection(double) - Static method in class etomica.statmech.HardSphereSolid
-
Returns the correction to high density expression for the
compressibility factor for solid (FCC) hard spheres at the given
density.
- zTriplePrime - Variable in class etomica.paracetamol.CoordinateDefinitionParacetamol
-
- zVecBox - Variable in class etomica.models.nitrogen.CalcHalfAnalyticHalfNumeric2ndDerivativeNitrogen
-
- zVecBox - Variable in class etomica.models.nitrogen.CalcNumerical2ndDerivativeNitrogen
-
- zVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- zVecBox - Variable in class etomica.models.nitrogen.HarmonicAlphaNitrogenModelPairMoleculeSequentialLS
-
- zVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequential5dofLS
-
- zVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialHalf2LS
-
- zVecBox - Variable in class etomica.models.nitrogen.HarmonicBetaNitrogenModelPairMoleculeSequentialLS
-
- zVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialHalf2LS
-
- zVecBox - Variable in class etomica.models.nitrogen.HarmonicDisorderedAlphaNitrogenModelPairMoleculeSequentialLS
-
- zVecBox - Variable in class etomica.models.nitrogen.MinimizationBetaNitrogenModelLS
-
- zWork - Variable in class etomica.models.water.OrientationCalcWater3P
-
- zWork - Variable in class etomica.models.water.OrientationCalcWater4P
-
- zx - Variable in class etomica.space3d.Tensor3D
-
- zy - Variable in class etomica.space3d.Tensor3D
-
- zz - Variable in class etomica.models.co2.PNCO2GCPM.P3GCPMAxilrodTeller
-
- zz - Variable in class etomica.models.co2.PNGCPM.P3GCPMAxilrodTeller
-
- zz - Variable in class etomica.space3d.Tensor3D
-
_
- _3dEnabled - Static variable in class etomica.graphics.DisplayPolytope
-
- _a - Variable in class g3dsys.images.Ellipse
-
- _c - Variable in class g3dsys.images.Axes
-
- _c - Variable in class g3dsys.images.Ball
-
- _c - Variable in class g3dsys.images.Box
-
- _c - Variable in class g3dsys.images.Ellipse
-
- _c - Variable in class g3dsys.images.Line
-
- _c - Variable in class g3dsys.images.Triangle
-
- _d - Variable in class g3dsys.images.Ball
-
- _d - Variable in class g3dsys.images.Bond
-
- _d - Variable in class g3dsys.images.Ellipse
-
- _gsys - Variable in class g3dsys.images.Figure
-
- _id - Variable in class g3dsys.images.Figure
-
- _p - Variable in class g3dsys.images.Ball
-
- _p - Variable in class g3dsys.images.Ellipse
-
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _
